25657329499

Committed 11 May 2026 07:49AM UTC coverage: 53.252% (+1.1%) from 52.184%

Build # 25657329499

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push

github

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web-flow

Commit Message

Merge pull request #78 from Nanopublication/feature/setting-driven-query-instances

feat(services): discover query API instances from nanopub setting

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89.74

src/main/java/org/nanopub/extra/setting/NanopubSetting.java

package org.nanopub.extra.setting;

import org.eclipse.rdf4j.common.exception.RDF4JException;
import org.eclipse.rdf4j.model.IRI;
import org.eclipse.rdf4j.model.Statement;
import org.eclipse.rdf4j.model.ValueFactory;
import org.eclipse.rdf4j.model.impl.SimpleValueFactory;
import org.eclipse.rdf4j.model.vocabulary.RDF;
import org.eclipse.rdf4j.model.vocabulary.RDFS;
import org.eclipse.rdf4j.rio.RDFFormat;
import org.nanopub.MalformedNanopubException;
import org.nanopub.Nanopub;
import org.nanopub.NanopubImpl;
import org.nanopub.vocabulary.NPX;

import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.io.Serializable;
import java.util.HashSet;
import java.util.Objects;
import java.util.Set;

/**
 * This class represents a nanopub setting, which includes various configurations.
 */
public class NanopubSetting implements Serializable {

    private static ValueFactory vf = SimpleValueFactory.getInstance();

    /**
     * System property naming a TriG file with a custom setting nanopub. Overrides the
     * bundled default setting when set (env var {@code NANOPUB_SETTING_FILE} also accepted).
     */
    public static final String SETTING_FILE_PROPERTY = "nanopub.setting.file";

    /**
     * Environment variable equivalent of {@link #SETTING_FILE_PROPERTY}.
     */
    public static final String SETTING_FILE_ENV = "NANOPUB_SETTING_FILE";

    private static volatile NanopubSetting defaultSetting;

    /**
     * Retrieves the default nanopub setting, honoring the {@code nanopub.setting.file}
     * system property and the {@code NANOPUB_SETTING_FILE} environment variable as
     * overrides. When neither is set, falls back to {@link #getLocalSetting()}.
     *
     * @return the default NanopubSetting object
     * @throws org.eclipse.rdf4j.common.exception.RDF4JException if there is an error with RDF4J operations.
     * @throws org.nanopub.MalformedNanopubException             if the nanopub is malformed.
     * @throws java.io.IOException                               if there is an error reading the input stream.
     */
    public static NanopubSetting getDefaultSetting() throws RDF4JException, MalformedNanopubException, IOException {
        if (defaultSetting != null) return defaultSetting;
        synchronized (NanopubSetting.class) {
            if (defaultSetting != null) return defaultSetting;
            String path = System.getProperty(SETTING_FILE_PROPERTY);
            if (path == null || path.isEmpty()) path = System.getenv(SETTING_FILE_ENV);
            if (path != null && !path.isEmpty()) {
                defaultSetting = new NanopubSetting(new NanopubImpl(new File(path)));
            } else {
                defaultSetting = getLocalSetting();
            }
            return defaultSetting;
        }
    }

    /**
     * Retrieves the default local nanopub setting.
     *
     * @return the NanopubSetting object for the default setting.
     * @throws org.eclipse.rdf4j.common.exception.RDF4JException if there is an error with RDF4J operations.
     * @throws org.nanopub.MalformedNanopubException             if the nanopub is malformed.
     * @throws java.io.IOException                               if there is an error reading the input stream.
     */
    public static NanopubSetting getLocalSetting() throws RDF4JException, MalformedNanopubException, IOException {
        return getLocalSetting(null);
    }

    /**
     * Retrieves the local nanopub setting by name.
     *
     * @param name the name of the setting, or "default" if null is provided.
     * @return the NanopubSetting object corresponding to the specified name.
     * @throws org.eclipse.rdf4j.common.exception.RDF4JException if there is an error with RDF4J operations.
     * @throws org.nanopub.MalformedNanopubException             if the nanopub is malformed.
     * @throws java.io.IOException                               if there is an error reading the input stream.
     */
    public static NanopubSetting getLocalSetting(String name) throws RDF4JException, MalformedNanopubException, IOException {
        if (name == null) name = "default";
        NanopubSetting setting = null;
        try (InputStream in = NanopubSetting.class.getResourceAsStream("/settings/" + name + ".trig")) {
            setting = new NanopubSetting(new NanopubImpl(in, RDFFormat.TRIG));
        }
        return setting;
    }

    private Nanopub nanopub;
    private IRI settingIri;
    private String name;
    private IRI agentIntroCollection;
    private IRI serviceIntroCollection;
    private Set<IRI> bootstrapServices = new HashSet<>();
    private IRI trustRangeAlgorithm;
    private IRI updateStrategy;

    /**
     * Constructs a NanopubSetting from a Nanopub object.
     *
     * @param nanopub the Nanopub object to create the setting from.
     */
    public NanopubSetting(Nanopub nanopub) {
        this.nanopub = nanopub;
        for (Statement st : nanopub.getAssertion()) {
            if (st.getPredicate().equals(RDF.TYPE) && st.getObject() instanceof IRI) {
                settingIri = (IRI) st.getSubject();
                break;
            }
        }
        if (settingIri == null) {
            throw new RuntimeException("No setting IRI found: " + nanopub.getUri());
        }
        for (Statement st : nanopub.getAssertion()) {
            if (!st.getSubject().equals(settingIri)) continue;
            IRI pred = st.getPredicate();
            if (pred.equals(RDFS.LABEL)) {
                name = st.getObject().stringValue();
                continue;
            }
            if (!(st.getObject() instanceof IRI obj)) continue;
            if (pred.equals(NPX.HAS_AGENTS)) {
                if (agentIntroCollection != null)
                    throw new RuntimeException("Two agent intro collections found: " + nanopub.getUri());
                agentIntroCollection = obj;
            } else if (pred.equals(NPX.HAS_SERVICES)) {
                if (serviceIntroCollection != null)
                    throw new RuntimeException("Two service intro collections found: " + nanopub.getUri());
                serviceIntroCollection = obj;
            } else if (pred.equals(NPX.HAS_BOOTSTRAP_SERVICE)) {
                bootstrapServices.add(obj);
            } else if (pred.equals(NPX.HAS_TRUST_RANGE_ALGORITHM)) {
                if (trustRangeAlgorithm != null)
                    throw new RuntimeException("Two trust range algorithms found: " + nanopub.getUri());
                trustRangeAlgorithm = obj;
            } else if (pred.equals(NPX.HAS_UPDATE_STRATEGY)) {
                if (updateStrategy != null)
                    throw new RuntimeException("Two update strategies found: " + nanopub.getUri());
                updateStrategy = obj;
            }
        }
    }

    /**
     * Returns the Nanopub object associated with this setting.
     *
     * @return the Nanopub object representing the setting.
     */
    public Nanopub getNanopub() {
        return nanopub;
    }

    /**
     * Returns the name of the setting.
     *
     * @return the name of the setting, or null if not set.
     */
    public String getName() {
        return name;
    }

    /**
     * Returns the IRI of the agent intro collection.
     *
     * @return the IRI of the agent intro collection, or null if not set.
     */
    public IRI getAgentIntroCollection() {
        return agentIntroCollection;
    }

    /**
     * Returns the IRI of the service intro collection.
     *
     * @return the IRI of the service intro collection, or null if not set.
     */
    public IRI getServiceIntroCollection() {
        return serviceIntroCollection;
    }

    /**
     * Returns a set of IRIs representing the bootstrap services.
     *
     * @return a set of IRIs for bootstrap services, which may be empty if none are defined.
     */
    public Set<IRI> getBootstrapServices() {
        return bootstrapServices;
    }

    /**
     * Returns the IRI of the trust range algorithm.
     *
     * @return the IRI of the trust range algorithm, or null if not set.
     */
    public IRI getTrustRangeAlgorithm() {
        return trustRangeAlgorithm;
    }

    /**
     * Returns the IRI of the update strategy.
     *
     * @return the IRI of the update strategy, or null if not set.
     */
    public IRI getUpdateStrategy() {
        return updateStrategy;
    }

    /**
     * {@inheritDoc}
     */
    @Override
    public boolean equals(Object o) {
        if (o == null || getClass() != o.getClass()) {
            return false;
        }
        NanopubSetting that = (NanopubSetting) o;
        return Objects.equals(nanopub, that.nanopub);
    }

    /**
     * {@inheritDoc}
     */
    @Override
    public int hashCode() {
        return Objects.hash(nanopub);
    }

}

1	package org.nanopub.extra.setting;
2
3	import org.eclipse.rdf4j.common.exception.RDF4JException;
4	import org.eclipse.rdf4j.model.IRI;
5	import org.eclipse.rdf4j.model.Statement;
6	import org.eclipse.rdf4j.model.ValueFactory;
7	import org.eclipse.rdf4j.model.impl.SimpleValueFactory;
8	import org.eclipse.rdf4j.model.vocabulary.RDF;
9	import org.eclipse.rdf4j.model.vocabulary.RDFS;
10	import org.eclipse.rdf4j.rio.RDFFormat;
11	import org.nanopub.MalformedNanopubException;
12	import org.nanopub.Nanopub;
13	import org.nanopub.NanopubImpl;
14	import org.nanopub.vocabulary.NPX;
15
16	import java.io.File;
17	import java.io.IOException;
18	import java.io.InputStream;
19	import java.io.Serializable;
20	import java.util.HashSet;
21	import java.util.Objects;
22	import java.util.Set;
23
24	/**
25	* This class represents a nanopub setting, which includes various configurations.
26	*/
27	public class NanopubSetting implements Serializable {
28
29	private static ValueFactory vf = SimpleValueFactory.getInstance();	9✔
30
31	/**
32	* System property naming a TriG file with a custom setting nanopub. Overrides the
33	* bundled default setting when set (env var {@code NANOPUB_SETTING_FILE} also accepted).
34	*/
35	public static final String SETTING_FILE_PROPERTY = "nanopub.setting.file";
36
37	/**
38	* Environment variable equivalent of {@link #SETTING_FILE_PROPERTY}.
39	*/
40	public static final String SETTING_FILE_ENV = "NANOPUB_SETTING_FILE";
41
42	private static volatile NanopubSetting defaultSetting;
43
44	/**
45	* Retrieves the default nanopub setting, honoring the {@code nanopub.setting.file}
46	* system property and the {@code NANOPUB_SETTING_FILE} environment variable as
47	* overrides. When neither is set, falls back to {@link #getLocalSetting()}.
48	*
49	* @return the default NanopubSetting object
50	* @throws org.eclipse.rdf4j.common.exception.RDF4JException if there is an error with RDF4J operations.
51	* @throws org.nanopub.MalformedNanopubException if the nanopub is malformed.
52	* @throws java.io.IOException if there is an error reading the input stream.
53	*/
54	public static NanopubSetting getDefaultSetting() throws RDF4JException, MalformedNanopubException, IOException {
55	if (defaultSetting != null) return defaultSetting;	12✔
56	synchronized (NanopubSetting.class) {	12✔
57	if (defaultSetting != null) return defaultSetting;	6!
58	String path = System.getProperty(SETTING_FILE_PROPERTY);	9✔
59	if (path == null \|\| path.isEmpty()) path = System.getenv(SETTING_FILE_ENV);	15!
60	if (path != null && !path.isEmpty()) {	6!
61	defaultSetting = new NanopubSetting(new NanopubImpl(new File(path)));	×
62	} else {
63	defaultSetting = getLocalSetting();	6✔
64	}
65	return defaultSetting;	12✔
66	}
67	}
68
69	/**
70	* Retrieves the default local nanopub setting.
71	*
72	* @return the NanopubSetting object for the default setting.
73	* @throws org.eclipse.rdf4j.common.exception.RDF4JException if there is an error with RDF4J operations.
74	* @throws org.nanopub.MalformedNanopubException if the nanopub is malformed.
75	* @throws java.io.IOException if there is an error reading the input stream.
76	*/
77	public static NanopubSetting getLocalSetting() throws RDF4JException, MalformedNanopubException, IOException {
78	return getLocalSetting(null);	9✔
79	}
80
81	/**
82	* Retrieves the local nanopub setting by name.
83	*
84	* @param name the name of the setting, or "default" if null is provided.
85	* @return the NanopubSetting object corresponding to the specified name.
86	* @throws org.eclipse.rdf4j.common.exception.RDF4JException if there is an error with RDF4J operations.
87	* @throws org.nanopub.MalformedNanopubException if the nanopub is malformed.
88	* @throws java.io.IOException if there is an error reading the input stream.
89	*/
90	public static NanopubSetting getLocalSetting(String name) throws RDF4JException, MalformedNanopubException, IOException {
91	if (name == null) name = "default";	12✔
92	NanopubSetting setting = null;	6✔
93	try (InputStream in = NanopubSetting.class.getResourceAsStream("/settings/" + name + ".trig")) {	15✔
94	setting = new NanopubSetting(new NanopubImpl(in, RDFFormat.TRIG));	27✔
95	}
96	return setting;	6✔
97	}
98
99	private Nanopub nanopub;
100	private IRI settingIri;
101	private String name;
102	private IRI agentIntroCollection;
103	private IRI serviceIntroCollection;
104	private Set<IRI> bootstrapServices = new HashSet<>();	15✔
105	private IRI trustRangeAlgorithm;
106	private IRI updateStrategy;
107
108	/**
109	* Constructs a NanopubSetting from a Nanopub object.
110	*
111	* @param nanopub the Nanopub object to create the setting from.
112	*/
113	public NanopubSetting(Nanopub nanopub) {	6✔
114	this.nanopub = nanopub;	9✔
115	for (Statement st : nanopub.getAssertion()) {	33✔
116	if (st.getPredicate().equals(RDF.TYPE) && st.getObject() instanceof IRI) {	27✔
117	settingIri = (IRI) st.getSubject();	15✔
118	break;	3✔
119	}
120	}	3✔
121	if (settingIri == null) {	9✔
122	throw new RuntimeException("No setting IRI found: " + nanopub.getUri());	24✔
123	}
124	for (Statement st : nanopub.getAssertion()) {	33✔
125	if (!st.getSubject().equals(settingIri)) continue;	21✔
126	IRI pred = st.getPredicate();	9✔
127	if (pred.equals(RDFS.LABEL)) {	12✔
128	name = st.getObject().stringValue();	15✔
129	continue;	3✔
130	}
131	if (!(st.getObject() instanceof IRI obj)) continue;	27✔
132	if (pred.equals(NPX.HAS_AGENTS)) {	12✔
133	if (agentIntroCollection != null)	9✔
134	throw new RuntimeException("Two agent intro collections found: " + nanopub.getUri());	24✔
135	agentIntroCollection = obj;	12✔
136	} else if (pred.equals(NPX.HAS_SERVICES)) {	12✔
137	if (serviceIntroCollection != null)	9✔
138	throw new RuntimeException("Two service intro collections found: " + nanopub.getUri());	24✔
139	serviceIntroCollection = obj;	12✔
140	} else if (pred.equals(NPX.HAS_BOOTSTRAP_SERVICE)) {	12✔
141	bootstrapServices.add(obj);	18✔
142	} else if (pred.equals(NPX.HAS_TRUST_RANGE_ALGORITHM)) {	12✔
143	if (trustRangeAlgorithm != null)	9✔
144	throw new RuntimeException("Two trust range algorithms found: " + nanopub.getUri());	24✔
145	trustRangeAlgorithm = obj;	12✔
146	} else if (pred.equals(NPX.HAS_UPDATE_STRATEGY)) {	12✔
147	if (updateStrategy != null)	9✔
148	throw new RuntimeException("Two update strategies found: " + nanopub.getUri());	24✔
149	updateStrategy = obj;	9✔
150	}
151	}	3✔
152	}	3✔
153
154	/**
155	* Returns the Nanopub object associated with this setting.
156	*
157	* @return the Nanopub object representing the setting.
158	*/
159	public Nanopub getNanopub() {
160	return nanopub;	9✔
161	}
162
163	/**
164	* Returns the name of the setting.
165	*
166	* @return the name of the setting, or null if not set.
167	*/
168	public String getName() {
169	return name;	9✔
170	}
171
172	/**
173	* Returns the IRI of the agent intro collection.
174	*
175	* @return the IRI of the agent intro collection, or null if not set.
176	*/
177	public IRI getAgentIntroCollection() {
178	return agentIntroCollection;	9✔
179	}
180
181	/**
182	* Returns the IRI of the service intro collection.
183	*
184	* @return the IRI of the service intro collection, or null if not set.
185	*/
186	public IRI getServiceIntroCollection() {
187	return serviceIntroCollection;	9✔
188	}
189
190	/**
191	* Returns a set of IRIs representing the bootstrap services.
192	*
193	* @return a set of IRIs for bootstrap services, which may be empty if none are defined.
194	*/
195	public Set<IRI> getBootstrapServices() {
196	return bootstrapServices;	9✔
197	}
198
199	/**
200	* Returns the IRI of the trust range algorithm.
201	*
202	* @return the IRI of the trust range algorithm, or null if not set.
203	*/
204	public IRI getTrustRangeAlgorithm() {
205	return trustRangeAlgorithm;	9✔
206	}
207
208	/**
209	* Returns the IRI of the update strategy.
210	*
211	* @return the IRI of the update strategy, or null if not set.
212	*/
213	public IRI getUpdateStrategy() {
214	return updateStrategy;	9✔
215	}
216
217	/**
218	* {@inheritDoc}
219	*/
220	@Override
221	public boolean equals(Object o) {
222	if (o == null \|\| getClass() != o.getClass()) {	21!
223	return false;	×
224	}
225	NanopubSetting that = (NanopubSetting) o;	9✔
226	return Objects.equals(nanopub, that.nanopub);	18✔
227	}
228
229	/**
230	* {@inheritDoc}
231	*/
232	@Override
233	public int hashCode() {
234	return Objects.hash(nanopub);	×
235	}
236
237	}

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