16986825439

Committed 15 Aug 2025 09:05AM UTC coverage: 25.779% (+3.1%) from 22.72%

Build # 16986825439

Build Type

push

github

Committed by

ashleycaselli

Commit Message

ci: update config to use maven wrapper

Run Details

122 of 494 branches covered (24.7%)

Branch coverage included in aggregate %.

333 of 1271 relevant lines covered (26.2%)

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81.08

src/main/java/com/knowledgepixels/query/Utils.java

package com.knowledgepixels.query;

import com.google.common.hash.Hashing;
import org.apache.commons.exec.environment.EnvironmentUtils;
import org.apache.commons.lang3.StringUtils;
import org.eclipse.rdf4j.model.IRI;
import org.eclipse.rdf4j.model.Value;
import org.eclipse.rdf4j.model.ValueFactory;
import org.eclipse.rdf4j.model.impl.SimpleValueFactory;
import org.eclipse.rdf4j.query.BindingSet;
import org.eclipse.rdf4j.query.QueryLanguage;
import org.eclipse.rdf4j.query.TupleQuery;
import org.eclipse.rdf4j.query.TupleQueryResult;
import org.eclipse.rdf4j.repository.RepositoryConnection;

import java.nio.charset.StandardCharsets;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;

/**
 * Utils class for Nanopub Registry.
 */
public class Utils {

    private Utils() {
    }  // no instances allowed

    private static final ValueFactory vf = SimpleValueFactory.getInstance();

    /**
     * IRI for the predicate that indicates that a hash value is associated with an object.
     */
    public static final IRI IS_HASH_OF = vf.createIRI("http://purl.org/nanopub/admin/isHashOf");

    /**
     * Prefix for the hash values stored in the admin graph.
     */
    public static final IRI HASH_PREFIX = vf.createIRI("http://purl.org/nanopub/admin/hash/");

    private static Map<String, Value> hashToObjMap;

    /**
     * Returns reverse hashing map.
     *
     * @return Map from hashes to their original objects
     */
    static Map<String, Value> getHashToObjectMap() {
        if (hashToObjMap == null) {
            hashToObjMap = new HashMap<>();
            try (RepositoryConnection conn = TripleStore.get().getAdminRepoConnection()) {
                TupleQuery query = conn.prepareTupleQuery(QueryLanguage.SPARQL, "SELECT * { graph ?g { ?s ?p ?o } }");
                query.setBinding("g", NanopubLoader.ADMIN_GRAPH);
                query.setBinding("p", IS_HASH_OF);
                try (TupleQueryResult r = query.evaluate()) {
                    while (r.hasNext()) {
                        BindingSet b = r.next();
                        String hash = b.getBinding("s").getValue().stringValue();
                        hash = StringUtils.replace(hash, HASH_PREFIX.toString(), "");
                        hashToObjMap.put(hash, b.getBinding("o").getValue());
                    }
                }
            }
        }
        return hashToObjMap;
    }

    /**
     * Returns the original object for the given hash value.
     *
     * @param hash The hash value
     * @return The original object
     */
    public static Value getObjectForHash(String hash) {
        return getHashToObjectMap().get(hash);
    }

    /**
     * Creates a hash value for the object and remembers it.
     *
     * @param obj Object to be hashed
     * @return hash value
     */
    public static String createHash(Object obj) {
        String hash = Hashing.sha256().hashString(obj.toString(), StandardCharsets.UTF_8).toString();

        if (!getHashToObjectMap().containsKey(hash)) {
            Value objV = getValue(obj);
            try (RepositoryConnection conn = TripleStore.get().getAdminRepoConnection()) {
                conn.add(vf.createStatement(vf.createIRI(HASH_PREFIX + hash), IS_HASH_OF, objV, NanopubLoader.ADMIN_GRAPH));
            }
            getHashToObjectMap().put(hash, objV);
        }
        return hash;
    }

    /**
     * Returns the object as a Value object.
     *
     * @param obj Input object
     * @return A Value object with the string content of the input object
     */
    static Value getValue(Object obj) {
        if (obj instanceof Value) {
            return (Value) obj;
        } else {
            return vf.createLiteral(obj.toString());
        }
    }

    /**
     * Returns a short "name" for the given public key
     *
     * @param pubkey Public key string
     * @return Short "name"
     */
    public static String getShortPubkeyName(String pubkey) {
        return pubkey.replaceFirst("^(.).{39}(.{5}).*$", "$1..$2..");
    }

    /**
     * Executes a query on the given connection to return the first objects matching the input.
     *
     * @param conn  The repository connection
     * @param graph Graph (=context) IRI
     * @param subj  Subject IRI
     * @param pred  Predicate IRI
     * @return the first object to match the pattern
     */
    public static Value getObjectForPattern(RepositoryConnection conn, IRI graph, IRI subj, IRI pred) {
        TupleQueryResult r = conn.prepareTupleQuery(QueryLanguage.SPARQL, "SELECT * { graph <" + graph.stringValue() + "> { <" + subj.stringValue() + "> <" + pred.stringValue() + "> ?o } }").evaluate();
        try (r) {
            if (!r.hasNext()) return null;
            return r.next().getBinding("o").getValue();
        }
    }

    /**
     * Executes a query on the given connection to return all objects matching the input.
     *
     * @param conn  The repository connection
     * @param graph Graph (=context) IRI
     * @param subj  Subject IRI
     * @param pred  Predicate IRI
     * @return a list of all objects matching the pattern
     */
    public static List<Value> getObjectsForPattern(RepositoryConnection conn, IRI graph, IRI subj, IRI pred) {
        List<Value> values = new ArrayList<>();
        TupleQueryResult r = conn.prepareTupleQuery(QueryLanguage.SPARQL, "SELECT * { graph <" + graph.stringValue() + "> { <" + subj.stringValue() + "> <" + pred.stringValue() + "> ?o } }").evaluate();
        try (r) {
            while (r.hasNext()) {
                values.add(r.next().getBinding("o").getValue());
            }
            return values;
        }
    }

    /**
     * Returns the system environment variable content for the given environment variable name.
     *
     * @param envVarName   environment variable name
     * @param defaultValue default value if not found
     * @return environment variable value
     */
    public static String getEnvString(String envVarName, String defaultValue) {
        try {
            String s = EnvironmentUtils.getProcEnvironment().get(envVarName);
            if (s != null && !s.isEmpty()) {
                return s;
            }
        } catch (Exception ex) {
            ex.printStackTrace();
        }
        return defaultValue;
    }

    /**
     * Returns the system environment variable content as an integer for the given environment variable name.
     *
     * @param envVarName   environment variable name
     * @param defaultValue default value if not found
     * @return environment variable value interpreted as an integer
     */
    public static int getEnvInt(String envVarName, int defaultValue) {
        try {
            String s = getEnvString(envVarName, null);
            if (s != null) {
                return Integer.parseInt(s);
            }
        } catch (Exception ex) {
            ex.printStackTrace();
        }
        return defaultValue;
    }

    /**
     * Default query to be shown in YASGUI client.
     */
    public static final String defaultQuery = """
            prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
            prefix dct: <http://purl.org/dc/terms/>
            prefix np: <http://www.nanopub.org/nschema#>
            prefix npa: <http://purl.org/nanopub/admin/>
            prefix npx: <http://purl.org/nanopub/x/>
            
            select * where {
            ## Info about this repo:
              npa:thisRepo ?pred ?obj .
            ## Search for nanopublications:
            # graph npa:graph {
            #   ?np npa:hasValidSignatureForPublicKey ?pubkey .
            #   filter not exists { ?npx npx:invalidates ?np ; npa:hasValidSignatureForPublicKey ?pubkey . }
            #   ?np dct:created ?date .
            #   ?np np:hasAssertion ?a .
            #   optional { ?np rdfs:label ?label }
            # }
            } limit 10""";

}

1	package com.knowledgepixels.query;
2
3	import com.google.common.hash.Hashing;
4	import org.apache.commons.exec.environment.EnvironmentUtils;
5	import org.apache.commons.lang3.StringUtils;
6	import org.eclipse.rdf4j.model.IRI;
7	import org.eclipse.rdf4j.model.Value;
8	import org.eclipse.rdf4j.model.ValueFactory;
9	import org.eclipse.rdf4j.model.impl.SimpleValueFactory;
10	import org.eclipse.rdf4j.query.BindingSet;
11	import org.eclipse.rdf4j.query.QueryLanguage;
12	import org.eclipse.rdf4j.query.TupleQuery;
13	import org.eclipse.rdf4j.query.TupleQueryResult;
14	import org.eclipse.rdf4j.repository.RepositoryConnection;
15
16	import java.nio.charset.StandardCharsets;
17	import java.util.ArrayList;
18	import java.util.HashMap;
19	import java.util.List;
20	import java.util.Map;
21
22	/**
23	* Utils class for Nanopub Registry.
24	*/
25	public class Utils {
26
27	private Utils() {
28	} // no instances allowed
29
30	private static final ValueFactory vf = SimpleValueFactory.getInstance();	2✔
31
32	/**
33	* IRI for the predicate that indicates that a hash value is associated with an object.
34	*/
35	public static final IRI IS_HASH_OF = vf.createIRI("http://purl.org/nanopub/admin/isHashOf");	4✔
36
37	/**
38	* Prefix for the hash values stored in the admin graph.
39	*/
40	public static final IRI HASH_PREFIX = vf.createIRI("http://purl.org/nanopub/admin/hash/");	5✔
41
42	private static Map<String, Value> hashToObjMap;
43
44	/**
45	* Returns reverse hashing map.
46	*
47	* @return Map from hashes to their original objects
48	*/
49	static Map<String, Value> getHashToObjectMap() {
50	if (hashToObjMap == null) {	2✔
51	hashToObjMap = new HashMap<>();	4✔
52	try (RepositoryConnection conn = TripleStore.get().getAdminRepoConnection()) {	×
53	TupleQuery query = conn.prepareTupleQuery(QueryLanguage.SPARQL, "SELECT * { graph ?g { ?s ?p ?o } }");	×
54	query.setBinding("g", NanopubLoader.ADMIN_GRAPH);	×
55	query.setBinding("p", IS_HASH_OF);	×
56	try (TupleQueryResult r = query.evaluate()) {	×
57	while (r.hasNext()) {	×
58	BindingSet b = r.next();	×
59	String hash = b.getBinding("s").getValue().stringValue();	×
60	hash = StringUtils.replace(hash, HASH_PREFIX.toString(), "");	×
61	hashToObjMap.put(hash, b.getBinding("o").getValue());	×
62	}	×
63	}
64	}
65	}
66	return hashToObjMap;	2✔
67	}
68
69	/**
70	* Returns the original object for the given hash value.
71	*
72	* @param hash The hash value
73	* @return The original object
74	*/
75	public static Value getObjectForHash(String hash) {
76	return getHashToObjectMap().get(hash);	5✔
77	}
78
79	/**
80	* Creates a hash value for the object and remembers it.
81	*
82	* @param obj Object to be hashed
83	* @return hash value
84	*/
85	public static String createHash(Object obj) {
86	String hash = Hashing.sha256().hashString(obj.toString(), StandardCharsets.UTF_8).toString();	7✔
87
88	if (!getHashToObjectMap().containsKey(hash)) {	4✔
89	Value objV = getValue(obj);	3✔
90	try (RepositoryConnection conn = TripleStore.get().getAdminRepoConnection()) {	3✔
91	conn.add(vf.createStatement(vf.createIRI(HASH_PREFIX + hash), IS_HASH_OF, objV, NanopubLoader.ADMIN_GRAPH));	15✔
92	}
93	getHashToObjectMap().put(hash, objV);	5✔
94	}
95	return hash;	2✔
96	}
97
98	/**
99	* Returns the object as a Value object.
100	*
101	* @param obj Input object
102	* @return A Value object with the string content of the input object
103	*/
104	static Value getValue(Object obj) {
105	if (obj instanceof Value) {	3✔
106	return (Value) obj;	3✔
107	} else {
108	return vf.createLiteral(obj.toString());	5✔
109	}
110	}
111
112	/**
113	* Returns a short "name" for the given public key
114	*
115	* @param pubkey Public key string
116	* @return Short "name"
117	*/
118	public static String getShortPubkeyName(String pubkey) {
119	return pubkey.replaceFirst("^(.).{39}(.{5}).*$", "$1..$2..");	5✔
120	}
121
122	/**
123	* Executes a query on the given connection to return the first objects matching the input.
124	*
125	* @param conn The repository connection
126	* @param graph Graph (=context) IRI
127	* @param subj Subject IRI
128	* @param pred Predicate IRI
129	* @return the first object to match the pattern
130	*/
131	public static Value getObjectForPattern(RepositoryConnection conn, IRI graph, IRI subj, IRI pred) {
132	TupleQueryResult r = conn.prepareTupleQuery(QueryLanguage.SPARQL, "SELECT * { graph <" + graph.stringValue() + "> { <" + subj.stringValue() + "> <" + pred.stringValue() + "> ?o } }").evaluate();	12✔
133	try (r) {	2✔
134	if (!r.hasNext()) return null;	7✔
135	return r.next().getBinding("o").getValue();	9✔
136	}	4!
137	}
138
139	/**
140	* Executes a query on the given connection to return all objects matching the input.
141	*
142	* @param conn The repository connection
143	* @param graph Graph (=context) IRI
144	* @param subj Subject IRI
145	* @param pred Predicate IRI
146	* @return a list of all objects matching the pattern
147	*/
148	public static List<Value> getObjectsForPattern(RepositoryConnection conn, IRI graph, IRI subj, IRI pred) {
149	List<Value> values = new ArrayList<>();	4✔
150	TupleQueryResult r = conn.prepareTupleQuery(QueryLanguage.SPARQL, "SELECT * { graph <" + graph.stringValue() + "> { <" + subj.stringValue() + "> <" + pred.stringValue() + "> ?o } }").evaluate();	12✔
151	try (r) {	2✔
152	while (r.hasNext()) {	3✔
153	values.add(r.next().getBinding("o").getValue());	10✔
154	}
155	return values;	4✔
156	}
157	}
158
159	/**
160	* Returns the system environment variable content for the given environment variable name.
161	*
162	* @param envVarName environment variable name
163	* @param defaultValue default value if not found
164	* @return environment variable value
165	*/
166	public static String getEnvString(String envVarName, String defaultValue) {
167	try {
168	String s = EnvironmentUtils.getProcEnvironment().get(envVarName);	5✔
169	if (s != null && !s.isEmpty()) {	5✔
170	return s;	2✔
171	}
172	} catch (Exception ex) {	1✔
173	ex.printStackTrace();	2✔
174	}	1✔
175	return defaultValue;	2✔
176	}
177
178	/**
179	* Returns the system environment variable content as an integer for the given environment variable name.
180	*
181	* @param envVarName environment variable name
182	* @param defaultValue default value if not found
183	* @return environment variable value interpreted as an integer
184	*/
185	public static int getEnvInt(String envVarName, int defaultValue) {
186	try {
187	String s = getEnvString(envVarName, null);	4✔
188	if (s != null) {	2✔
189	return Integer.parseInt(s);	3✔
190	}
191	} catch (Exception ex) {	1✔
192	ex.printStackTrace();	2✔
193	}	1✔
194	return defaultValue;	2✔
195	}
196
197	/**
198	* Default query to be shown in YASGUI client.
199	*/
200	public static final String defaultQuery = """
201	prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
202	prefix dct: <http://purl.org/dc/terms/>
203	prefix np: <http://www.nanopub.org/nschema#>
204	prefix npa: <http://purl.org/nanopub/admin/>
205	prefix npx: <http://purl.org/nanopub/x/>
206
207	select * where {
208	## Info about this repo:
209	npa:thisRepo ?pred ?obj .
210	## Search for nanopublications:
211	# graph npa:graph {
212	# ?np npa:hasValidSignatureForPublicKey ?pubkey .
213	# filter not exists { ?npx npx:invalidates ?np ; npa:hasValidSignatureForPublicKey ?pubkey . }
214	# ?np dct:created ?date .
215	# ?np np:hasAssertion ?a .
216	# optional { ?np rdfs:label ?label }
217	# }
218	} limit 10""";
219
220	}

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