17038267114

Committed 18 Aug 2025 10:41AM UTC coverage: 47.35% (-1.7%) from 49.072%

Build Type

push

github

Committed by Ziroli Plutschow

Commit Message

Now all Unit Tests run successful without network connection.

- Moved the GetIndex test to an Integration Test.

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881 of 2880 branches covered (30.59%)

Branch coverage included in aggregate %.

4729 of 8968 relevant lines covered (52.73%)

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78.47

src/main/java/org/nanopub/CustomTrigWriter.java

package org.nanopub;

import org.apache.commons.io.output.NullOutputStream;
import org.eclipse.rdf4j.model.IRI;
import org.eclipse.rdf4j.model.Literal;
import org.eclipse.rdf4j.model.util.Literals;
import org.eclipse.rdf4j.model.vocabulary.XSD;
import org.eclipse.rdf4j.rio.trig.TriGWriter;
import org.eclipse.rdf4j.rio.turtle.TurtleUtil;

import java.io.IOException;
import java.io.OutputStream;
import java.io.Writer;
import java.util.Set;

/**
 * Custom TriG writer that allows for the use of custom prefixes.
 *
 * @author Tobias Kuhn
 */
public class CustomTrigWriter extends TriGWriter {

    private Set<String> usedPrefixes;

    /**
     * Creates a new TriG writer that writes to the specified output stream.
     *
     * @param out The output stream to write to.
     */
    public CustomTrigWriter(OutputStream out) {
        super(out);
    }

    /**
     * Creates a new TriG writer that writes to the specified writer.
     *
     * @param writer The writer to write to.
     */
    public CustomTrigWriter(Writer writer) {
        super(writer);
    }

    /**
     * Creates a new TriG writer that uses the specified set of prefixes.
     *
     * @param out          The output stream to write to.
     * @param usedPrefixes The set of prefixes that are used in the document.
     */
    public CustomTrigWriter(OutputStream out, Set<String> usedPrefixes) {
        super(out);
        this.usedPrefixes = usedPrefixes;
    }

    /**
     * Creates a new TriG writer that uses the specified set of prefixes.
     *
     * @param writer       The writer to write to.
     * @param usedPrefixes The set of prefixes that are used in the document.
     */
    public CustomTrigWriter(Writer writer, Set<String> usedPrefixes) {
        super(writer);
        this.usedPrefixes = usedPrefixes;
    }

    /**
     * Creates a new TriG writer that uses the specified set of prefixes.
     *
     * @param usedPrefixes The set of prefixes that are used in the document.
     */
    public CustomTrigWriter(Set<String> usedPrefixes) {
        super(NullOutputStream.INSTANCE);
        this.usedPrefixes = usedPrefixes;
    }

    /**
     * {@inheritDoc}
     */
    @Override
    protected void writeURI(IRI uri) throws IOException {
        String uriString = uri.toString();

        String prefix = namespaceTable.get(uriString);
        if (prefix != null) {
            // Exact match: no suffix required
            writer.write(prefix);
            writer.write(":");
            if (usedPrefixes != null) {
                usedPrefixes.add(prefix);
            }
            return;
        }

        prefix = null;

        int splitIdx = TurtleUtil.findURISplitIndex(uriString);

        // Sesame bug for URIs that end with a period.
        // Port fix from https://bitbucket.org/openrdf/sesame/pull-request/301/ses-2086-fix-turtlewriter-writing/diff
        if (!TurtleUtil.isNameEndChar(uriString.charAt(uriString.length() - 1))) {
            splitIdx = -1;
        }

        if (splitIdx > 0) {
            String namespace = uriString.substring(0, splitIdx);
            prefix = namespaceTable.get(namespace);
        }

        // Do also split at dots:
        int splitIdxDot = uriString.lastIndexOf(".") + 1;
        if (uriString.length() == splitIdxDot) splitIdxDot = -1;
        if (splitIdx > 0 && splitIdxDot > splitIdx) {
            String namespace = uriString.substring(0, splitIdxDot);
            String p = namespaceTable.get(namespace);
            if (p != null) {
                splitIdx = splitIdxDot;
                prefix = p;
            }
        }

        // ... and colons:
        int splitIdxColon = uriString.lastIndexOf(":") + 1;
        if (uriString.length() == splitIdxColon) splitIdxColon = -1;
        if (splitIdx > 0 && splitIdxColon > splitIdx) {
            String namespace = uriString.substring(0, splitIdxColon);
            String p = namespaceTable.get(namespace);
            if (p != null) {
                splitIdx = splitIdxColon;
                prefix = p;
            }
        }

        // ... and underscores:
        int splitIdxUnderscore = uriString.lastIndexOf("_") + 1;
        if (uriString.length() == splitIdxUnderscore) splitIdxUnderscore = -1;
        if (splitIdx > 0 && splitIdxUnderscore > splitIdx) {
            String namespace = uriString.substring(0, splitIdxUnderscore);
            String p = namespaceTable.get(namespace);
            if (p != null) {
                splitIdx = splitIdxUnderscore;
                prefix = p;
            }
        }

        // ... and *before* hash signs:
        int splitIdxHashsign = uriString.lastIndexOf("#");
        if (splitIdx > 0 && splitIdxHashsign > splitIdx - 2) {
            String namespace = uriString.substring(0, splitIdxHashsign);
            String p = namespaceTable.get(namespace);
            String postHashPrefix = namespaceTable.get(namespace + "#");
            if (p != null && postHashPrefix == null) {
                splitIdx = splitIdxHashsign;
                prefix = p;
            }
        }

        if (uriString.endsWith(".")) {
            prefix = null;
        }

        if (prefix != null) {
            // Namespace is mapped to a prefix; write abbreviated URI
            writer.write(prefix);
            writer.write(":");
            writer.write(uriString.substring(splitIdx).replaceFirst("^#", "\\\\#"));
            if (usedPrefixes != null) {
                usedPrefixes.add(prefix);
            }
        } else {
            // Write full URI
            writer.write("<");
            writer.write(TurtleUtil.encodeURIString(uriString));
            writer.write(">");
        }
    }

    // Overriding this method to *not* normalize/pretty-print literals.

    /**
     * {@inheritDoc}
     */
    @Override
    protected void writeLiteral(Literal lit) throws IOException {
        String label = lit.getLabel();
        IRI datatype = lit.getDatatype();

        if (label.indexOf('\n') != -1 || label.indexOf('\r') != -1 || label.indexOf('\t') != -1) {
            // Write label as long string
            writer.write("\"\"\"");
            writer.write(TurtleUtil.encodeLongString(label));
            writer.write("\"\"\"");
        } else {
            // Write label as normal string
            writer.write("\"");
            writer.write(TurtleUtil.encodeString(label));
            writer.write("\"");
        }

        if (Literals.isLanguageLiteral(lit)) {
            // Append the literal's language
            writer.write("@");
            writer.write(lit.getLanguage().get());
        } else if (!XSD.STRING.equals(datatype)) {
            // Append the literal's datatype (possibly written as an abbreviated
            // URI)
            writer.write("^^");
            writeURI(datatype);
        }
    }
}

1	package org.nanopub;
2
3	import org.apache.commons.io.output.NullOutputStream;
4	import org.eclipse.rdf4j.model.IRI;
5	import org.eclipse.rdf4j.model.Literal;
6	import org.eclipse.rdf4j.model.util.Literals;
7	import org.eclipse.rdf4j.model.vocabulary.XSD;
8	import org.eclipse.rdf4j.rio.trig.TriGWriter;
9	import org.eclipse.rdf4j.rio.turtle.TurtleUtil;
10
11	import java.io.IOException;
12	import java.io.OutputStream;
13	import java.io.Writer;
14	import java.util.Set;
15
16	/**
17	* Custom TriG writer that allows for the use of custom prefixes.
18	*
19	* @author Tobias Kuhn
20	*/
21	public class CustomTrigWriter extends TriGWriter {
22
23	private Set<String> usedPrefixes;
24
25	/**
26	* Creates a new TriG writer that writes to the specified output stream.
27	*
28	* @param out The output stream to write to.
29	*/
30	public CustomTrigWriter(OutputStream out) {
31	super(out);	×
32	}	×
33
34	/**
35	* Creates a new TriG writer that writes to the specified writer.
36	*
37	* @param writer The writer to write to.
38	*/
39	public CustomTrigWriter(Writer writer) {
40	super(writer);	3✔
41	}	1✔
42
43	/**
44	* Creates a new TriG writer that uses the specified set of prefixes.
45	*
46	* @param out The output stream to write to.
47	* @param usedPrefixes The set of prefixes that are used in the document.
48	*/
49	public CustomTrigWriter(OutputStream out, Set<String> usedPrefixes) {
50	super(out);	×
51	this.usedPrefixes = usedPrefixes;	×
52	}	×
53
54	/**
55	* Creates a new TriG writer that uses the specified set of prefixes.
56	*
57	* @param writer The writer to write to.
58	* @param usedPrefixes The set of prefixes that are used in the document.
59	*/
60	public CustomTrigWriter(Writer writer, Set<String> usedPrefixes) {
61	super(writer);	×
62	this.usedPrefixes = usedPrefixes;	×
63	}	×
64
65	/**
66	* Creates a new TriG writer that uses the specified set of prefixes.
67	*
68	* @param usedPrefixes The set of prefixes that are used in the document.
69	*/
70	public CustomTrigWriter(Set<String> usedPrefixes) {
71	super(NullOutputStream.INSTANCE);	3✔
72	this.usedPrefixes = usedPrefixes;	3✔
73	}	1✔
74
75	/**
76	* {@inheritDoc}
77	*/
78	@Override
79	protected void writeURI(IRI uri) throws IOException {
80	String uriString = uri.toString();	3✔
81
82	String prefix = namespaceTable.get(uriString);	6✔
83	if (prefix != null) {	2✔
84	// Exact match: no suffix required
85	writer.write(prefix);	4✔
86	writer.write(":");	4✔
87	if (usedPrefixes != null) {	3✔
88	usedPrefixes.add(prefix);	5✔
89	}
90	return;	1✔
91	}
92
93	prefix = null;	2✔
94
95	int splitIdx = TurtleUtil.findURISplitIndex(uriString);	3✔
96
97	// Sesame bug for URIs that end with a period.
98	// Port fix from https://bitbucket.org/openrdf/sesame/pull-request/301/ses-2086-fix-turtlewriter-writing/diff
99	if (!TurtleUtil.isNameEndChar(uriString.charAt(uriString.length() - 1))) {	8✔
100	splitIdx = -1;	2✔
101	}
102
103	if (splitIdx > 0) {	2✔
104	String namespace = uriString.substring(0, splitIdx);	5✔
105	prefix = namespaceTable.get(namespace);	6✔
106	}
107
108	// Do also split at dots:
109	int splitIdxDot = uriString.lastIndexOf(".") + 1;	6✔
110	if (uriString.length() == splitIdxDot) splitIdxDot = -1;	6✔
111	if (splitIdx > 0 && splitIdxDot > splitIdx) {	5✔
112	String namespace = uriString.substring(0, splitIdxDot);	5✔
113	String p = namespaceTable.get(namespace);	6✔
114	if (p != null) {	2!
115	splitIdx = splitIdxDot;	×
116	prefix = p;	×
117	}
118	}
119
120	// ... and colons:
121	int splitIdxColon = uriString.lastIndexOf(":") + 1;	6✔
122	if (uriString.length() == splitIdxColon) splitIdxColon = -1;	4!
123	if (splitIdx > 0 && splitIdxColon > splitIdx) {	5!
124	String namespace = uriString.substring(0, splitIdxColon);	×
125	String p = namespaceTable.get(namespace);	×
126	if (p != null) {	×
127	splitIdx = splitIdxColon;	×
128	prefix = p;	×
129	}
130	}
131
132	// ... and underscores:
133	int splitIdxUnderscore = uriString.lastIndexOf("_") + 1;	6✔
134	if (uriString.length() == splitIdxUnderscore) splitIdxUnderscore = -1;	4!
135	if (splitIdx > 0 && splitIdxUnderscore > splitIdx) {	5✔
136	String namespace = uriString.substring(0, splitIdxUnderscore);	5✔
137	String p = namespaceTable.get(namespace);	6✔
138	if (p != null) {	2!
139	splitIdx = splitIdxUnderscore;	×
140	prefix = p;	×
141	}
142	}
143
144	// ... and before hash signs:
145	int splitIdxHashsign = uriString.lastIndexOf("#");	4✔
146	if (splitIdx > 0 && splitIdxHashsign > splitIdx - 2) {	7✔
147	String namespace = uriString.substring(0, splitIdxHashsign);	5✔
148	String p = namespaceTable.get(namespace);	6✔
149	String postHashPrefix = namespaceTable.get(namespace + "#");	7✔
150	if (p != null && postHashPrefix == null) {	4!
151	splitIdx = splitIdxHashsign;	×
152	prefix = p;	×
153	}
154	}
155
156	if (uriString.endsWith(".")) {	4✔
157	prefix = null;	2✔
158	}
159
160	if (prefix != null) {	2✔
161	// Namespace is mapped to a prefix; write abbreviated URI
162	writer.write(prefix);	4✔
163	writer.write(":");	4✔
164	writer.write(uriString.substring(splitIdx).replaceFirst("^#", "\\\\#"));	9✔
165	if (usedPrefixes != null) {	3✔
166	usedPrefixes.add(prefix);	6✔
167	}
168	} else {
169	// Write full URI
170	writer.write("<");	4✔
171	writer.write(TurtleUtil.encodeURIString(uriString));	5✔
172	writer.write(">");	4✔
173	}
174	}	1✔
175
176	// Overriding this method to not normalize/pretty-print literals.
177
178	/**
179	* {@inheritDoc}
180	*/
181	@Override
182	protected void writeLiteral(Literal lit) throws IOException {
183	String label = lit.getLabel();	3✔
184	IRI datatype = lit.getDatatype();	3✔
185
186	if (label.indexOf('\n') != -1 \|\| label.indexOf('\r') != -1 \|\| label.indexOf('\t') != -1) {	15!
187	// Write label as long string
188	writer.write("\"\"\"");	4✔
189	writer.write(TurtleUtil.encodeLongString(label));	5✔
190	writer.write("\"\"\"");	5✔
191	} else {
192	// Write label as normal string
193	writer.write("\"");	4✔
194	writer.write(TurtleUtil.encodeString(label));	5✔
195	writer.write("\"");	4✔
196	}
197
198	if (Literals.isLanguageLiteral(lit)) {	3!
199	// Append the literal's language
200	writer.write("@");	×
201	writer.write(lit.getLanguage().get());	×
202	} else if (!XSD.STRING.equals(datatype)) {	4✔
203	// Append the literal's datatype (possibly written as an abbreviated
204	// URI)
205	writer.write("^^");	4✔
206	writeURI(datatype);	3✔
207	}
208	}	1✔
209	}

Nanopublication / nanopub-java / 17038267114

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