17767759901

Committed 16 Sep 2025 01:40PM UTC coverage: 71.59% (-0.2%) from 71.741%

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push

github

Committed by Ziroli Plutschow

Commit Message

Replacing newest System.err with slf4j logging

- Note: Also upgraded mockito, since it's transient dependency byte-buddy could not handle a jvm > 21

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233 of 350 branches covered (66.57%)

Branch coverage included in aggregate %.

591 of 801 relevant lines covered (73.78%)

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60.0

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

package com.knowledgepixels.query;

import java.util.ArrayList;
import java.util.Collections;
import java.util.Comparator;
import java.util.HashSet;
import java.util.List;
import java.util.Set;

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.DCTERMS;
import org.eclipse.rdf4j.model.vocabulary.RDFS;
import org.eclipse.rdf4j.query.algebra.Var;
import org.eclipse.rdf4j.query.algebra.helpers.AbstractSimpleQueryModelVisitor;
import org.eclipse.rdf4j.query.parser.ParsedQuery;
import org.eclipse.rdf4j.query.parser.sparql.SPARQLParser;
import org.nanopub.Nanopub;
import org.nanopub.SimpleCreatorPattern;
import org.nanopub.extra.server.GetNanopub;
import org.nanopub.extra.services.QueryAccess;

import io.vertx.core.MultiMap;
import net.trustyuri.TrustyUriUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

/**
 * This class produces a page with the grlc specification. This is needed internally to tell grlc
 * how to execute a particular query template.
 */
public class GrlcSpec {

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

    private static final Logger log = LoggerFactory.getLogger(GrlcSpec.class);

    /**
     * IRI for relation to link a grlc query instance to its SPARQL template.
     */
    public static final IRI HAS_SPARQL = vf.createIRI("https://w3id.org/kpxl/grlc/sparql");

    /**
     * IRI for relation to link a grlc query instance to its SPARQL endpoint URL.
     */
    public static final IRI HAS_ENDPOINT = vf.createIRI("https://w3id.org/kpxl/grlc/endpoint");

    /**
     * URL for the given Nanopub Query instance, needed for internal coordination.
     */
    public static final String nanopubQueryUrl = Utils.getEnvString("NANOPUB_QUERY_URL", "http://query:9393/");

    private MultiMap parameters;
    private Nanopub np;
    private String requestUrlBase;
    private String artifactCode, queryPart;
    private String queryName;
    private String label;
    private String desc;
    private String license;
    private String queryContent;
    private String endpoint;
    private List<String> placeholdersList;

    /**
     * Creates a new page instance.
     *
     * @param requestUrl The request URL
     * @param parameters The URL request parameters
     */
    public GrlcSpec(String requestUrl, MultiMap parameters) {
        requestUrl = requestUrl.replaceFirst("\\?.*$", "");
        this.parameters = parameters;
        if (!requestUrl.matches(".*/RA[A-Za-z0-9\\-_]{43}/(.*)?")) {
            // TODO Raise exception
            return;
        }
        artifactCode = requestUrl.replaceFirst("^(.*/)(RA[A-Za-z0-9\\-_]{43})/(.*)?$", "$2");
        queryPart = requestUrl.replaceFirst("^(.*/)(RA[A-Za-z0-9\\-_]{43}/)(.*)?$", "$3");
        requestUrlBase = requestUrl.replaceFirst("^/(.*/)(RA[A-Za-z0-9\\-_]{43})/(.*)?$", "$1");

        // TODO Get the nanopub from the local store:
        np = GetNanopub.get(artifactCode);
        if (parameters.get("api-version") != null && parameters.get("api-version").equals("latest")) {
            // TODO Get the latest version from the local store:
            np = GetNanopub.get(QueryAccess.getLatestVersionId(np.getUri().stringValue()));
            artifactCode = TrustyUriUtils.getArtifactCode(np.getUri().stringValue());
        }
        for (Statement st : np.getAssertion()) {
            if (!st.getSubject().stringValue().startsWith(np.getUri().stringValue())) continue;
            String qn = st.getSubject().stringValue().replaceFirst("^.*[#/](.*)$", "$1");
            if (queryName != null && !qn.equals(queryName)) {
                np = null;
                break;
            }
            queryName = qn;
            if (st.getPredicate().equals(RDFS.LABEL)) {
                label = st.getObject().stringValue();
            } else if (st.getPredicate().equals(DCTERMS.DESCRIPTION)) {
                desc = st.getObject().stringValue();
            } else if (st.getPredicate().equals(DCTERMS.LICENSE) && st.getObject() instanceof IRI) {
                license = st.getObject().stringValue();
            } else if (st.getPredicate().equals(HAS_SPARQL)) {
                // TODO Improve this:
                queryContent = st.getObject().stringValue().replace("https://w3id.org/np/l/nanopub-query-1.1/repo/", nanopubQueryUrl + "repo/");
            } else if (st.getPredicate().equals(HAS_ENDPOINT) && st.getObject() instanceof IRI) {
                endpoint = st.getObject().stringValue();
                if (endpoint.startsWith("https://w3id.org/np/l/nanopub-query-1.1/repo/")) {
                    endpoint = endpoint.replace("https://w3id.org/np/l/nanopub-query-1.1/repo/", nanopubQueryUrl + "repo/");
                } else {
                    // TODO Raise exception
                    endpoint = null;
                }
            }
        }

        final Set<String> placeholders = new HashSet<>();
        // TODO Make sure we properly handle MalformedQueryException thrown here:
        ParsedQuery query = new SPARQLParser().parseQuery(queryContent, null);
        query.getTupleExpr().visitChildren(new AbstractSimpleQueryModelVisitor<>() {

            @Override
            public void meet(Var node) throws RuntimeException {
                super.meet(node);
                if (!node.isConstant() && !node.isAnonymous() && node.getName().startsWith("_")) {
                    placeholders.add(node.getName());
                }
            }

        });
        List<String> placeholdersListPre = new ArrayList<>(placeholders);
        Collections.sort(placeholdersListPre);
        placeholdersListPre.sort(Comparator.comparing(String::length));
        placeholdersList = Collections.unmodifiableList(placeholdersListPre);
    }

    /**
     * Returns the grlc spec as a string.
     *
     * @return grlc specification string
     */
    public String getSpec() {
        if (np == null) return null;
        String s = "";
        if (queryPart.isEmpty()) {
            if (label == null) {
                s += "title: \"untitled query\"\n";
            } else {
                s += "title: \"" + escapeLiteral(label) + "\"\n";
            }
            s += "description: \"" + escapeLiteral(desc) + "\"\n";
            StringBuilder userName = new StringBuilder();
            Set<IRI> creators = SimpleCreatorPattern.getCreators(np);
            for (IRI userIri : creators) {
                userName.append(", ").append(userIri);
            }
            if (!userName.isEmpty()) userName = new StringBuilder(userName.substring(2));
            String url = "";
            if (!creators.isEmpty()) url = creators.iterator().next().stringValue();
            s += "contact:\n";
            s += "  name: \"" + escapeLiteral(userName.toString()) + "\"\n";
            s += "  url: " + url + "\n";
            if (license != null) {
                s += "licence: " + license + "\n";
            }
            s += "queries:\n";
            s += "  - " + nanopubQueryUrl + requestUrlBase + artifactCode + "/" + queryName + ".rq";
        } else if (queryPart.equals(queryName + ".rq")) {
            if (label != null) {
                s += "#+ summary: \"" + escapeLiteral(label) + "\"\n";
            }
            if (desc != null) {
                s += "#+ description: \"" + escapeLiteral(desc) + "\"\n";
            }
            if (license != null) {
                s += "#+ licence: " + license + "\n";
            }
            if (endpoint != null) {
                s += "#+ endpoint: " + endpoint + "\n";
            }
            s += "\n";
            s += queryContent;
        } else {
            return null;
        }
        return s;
    }

    public String getRepoName() {
        return endpoint.replaceAll("/", "_").replaceFirst("^.*_repo_", "");
    }

    public String getQueryContent() {
        return queryContent;
    }

    public String getExpandedQueryContent() {
        String expanded = queryContent;
        for (String ph : placeholdersList) {
            log.info("ph: ", ph);
            log.info("getParamName(ph): ", getParamName(ph));
            if (isMultiPlaceholder(ph)) {
                // TODO multi placeholders need proper documentation
                List<String> val = parameters.getAll(getParamName(ph));
                if (!isOptionalPlaceholder(ph) && val.isEmpty()) {
                    // TODO throw exception
                    return null;
                }
                if (val.isEmpty()) {
                    expanded = expanded.replaceAll("values\\s*\\?" + ph + "\\s*\\{\\s*\\}(\\s*\\.)?", "");
                    continue;
                }
                String valueList = "";
                for (String v : val) {
                    if (isIriPlaceholder(ph)) {
                        valueList += serializeIri(v) + " ";
                    } else {
                        valueList += serializeLiteral(v) + " ";
                    }
                }
                expanded = expanded.replaceAll("values\\s*\\?" + ph + "\\s*\\{\\s*\\}", "values ?" + ph + " { " + valueList + "}");
            } else {
                String val = parameters.get(getParamName(ph));
                log.info("val: ", val);
                if (!isOptionalPlaceholder(ph) && val == null) {
                    // TODO throw exception
                    return null;
                }
                if (val == null) continue;
                if (isIriPlaceholder(ph)) {
                    expanded = expanded.replaceAll("\\?" + ph, serializeIri(val));
                } else {
                    expanded = expanded.replaceAll("\\?" + ph, serializeLiteral(val));
                }
            }
        }
        log.info("expanded: ", expanded);
        return expanded;
    }

    public static String escapeLiteral(String s) {
        return s.replace("\\", "\\\\").replace("\n", "\\n").replace("\"", "\\\"");
    }

    public static boolean isOptionalPlaceholder(String placeholder) {
        return placeholder.startsWith("__");
    }

    public static boolean isMultiPlaceholder(String placeholder) {
        return placeholder.endsWith("_multi") || placeholder.endsWith("_multi_iri");
    }

    public static boolean isIriPlaceholder(String placeholder) {
        return placeholder.endsWith("_iri");
    }

    public static String getParamName(String placeholder) {
        return placeholder.replaceFirst("^_+", "").replaceFirst("_iri$", "").replaceFirst("_multi$", "");
    }

    public static String serializeIri(String iriString) {
        return "<" + iriString + ">";
    }

    public static String serializeLiteral(String literalString) {
        return "\"" + escapeLiteral(literalString) + "\"";
    }

}

1	package com.knowledgepixels.query;
2
3	import java.util.ArrayList;
4	import java.util.Collections;
5	import java.util.Comparator;
6	import java.util.HashSet;
7	import java.util.List;
8	import java.util.Set;
9
10	import org.eclipse.rdf4j.model.IRI;
11	import org.eclipse.rdf4j.model.Statement;
12	import org.eclipse.rdf4j.model.ValueFactory;
13	import org.eclipse.rdf4j.model.impl.SimpleValueFactory;
14	import org.eclipse.rdf4j.model.vocabulary.DCTERMS;
15	import org.eclipse.rdf4j.model.vocabulary.RDFS;
16	import org.eclipse.rdf4j.query.algebra.Var;
17	import org.eclipse.rdf4j.query.algebra.helpers.AbstractSimpleQueryModelVisitor;
18	import org.eclipse.rdf4j.query.parser.ParsedQuery;
19	import org.eclipse.rdf4j.query.parser.sparql.SPARQLParser;
20	import org.nanopub.Nanopub;
21	import org.nanopub.SimpleCreatorPattern;
22	import org.nanopub.extra.server.GetNanopub;
23	import org.nanopub.extra.services.QueryAccess;
24
25	import io.vertx.core.MultiMap;
26	import net.trustyuri.TrustyUriUtils;
27	import org.slf4j.Logger;
28	import org.slf4j.LoggerFactory;
29
30	/**
31	* This class produces a page with the grlc specification. This is needed internally to tell grlc
32	* how to execute a particular query template.
33	*/
34	public class GrlcSpec {
35
36	private static final ValueFactory vf = SimpleValueFactory.getInstance();	2✔
37
38	private static final Logger log = LoggerFactory.getLogger(GrlcSpec.class);	3✔
39
40	/**
41	* IRI for relation to link a grlc query instance to its SPARQL template.
42	*/
43	public static final IRI HAS_SPARQL = vf.createIRI("https://w3id.org/kpxl/grlc/sparql");	4✔
44
45	/**
46	* IRI for relation to link a grlc query instance to its SPARQL endpoint URL.
47	*/
48	public static final IRI HAS_ENDPOINT = vf.createIRI("https://w3id.org/kpxl/grlc/endpoint");	4✔
49
50	/**
51	* URL for the given Nanopub Query instance, needed for internal coordination.
52	*/
53	public static final String nanopubQueryUrl = Utils.getEnvString("NANOPUB_QUERY_URL", "http://query:9393/");	5✔
54
55	private MultiMap parameters;
56	private Nanopub np;
57	private String requestUrlBase;
58	private String artifactCode, queryPart;
59	private String queryName;
60	private String label;
61	private String desc;
62	private String license;
63	private String queryContent;
64	private String endpoint;
65	private List<String> placeholdersList;
66
67	/**
68	* Creates a new page instance.
69	*
70	* @param requestUrl The request URL
71	* @param parameters The URL request parameters
72	*/
73	public GrlcSpec(String requestUrl, MultiMap parameters) {	2✔
74	requestUrl = requestUrl.replaceFirst("\\?.*$", "");	5✔
75	this.parameters = parameters;	3✔
76	if (!requestUrl.matches("./RA[A-Za-z0-9\\-_]{43}/(.)?")) {	4✔
77	// TODO Raise exception
78	return;	1✔
79	}
80	artifactCode = requestUrl.replaceFirst("^(./)(RA[A-Za-z0-9\\-_]{43})/(.)?$", "$2");	6✔
81	queryPart = requestUrl.replaceFirst("^(./)(RA[A-Za-z0-9\\-_]{43}/)(.)?$", "$3");	6✔
82	requestUrlBase = requestUrl.replaceFirst("^/(./)(RA[A-Za-z0-9\\-_]{43})/(.)?$", "$1");	6✔
83
84	// TODO Get the nanopub from the local store:
85	np = GetNanopub.get(artifactCode);	5✔
86	if (parameters.get("api-version") != null && parameters.get("api-version").equals("latest")) {	10✔
87	// TODO Get the latest version from the local store:
88	np = GetNanopub.get(QueryAccess.getLatestVersionId(np.getUri().stringValue()));	8✔
89	artifactCode = TrustyUriUtils.getArtifactCode(np.getUri().stringValue());	7✔
90	}
91	for (Statement st : np.getAssertion()) {	12✔
92	if (!st.getSubject().stringValue().startsWith(np.getUri().stringValue())) continue;	9!
93	String qn = st.getSubject().stringValue().replaceFirst("^.[#/](.)$", "$1");	7✔
94	if (queryName != null && !qn.equals(queryName)) {	8!
95	np = null;	×
96	break;	×
97	}
98	queryName = qn;	3✔
99	if (st.getPredicate().equals(RDFS.LABEL)) {	5✔
100	label = st.getObject().stringValue();	6✔
101	} else if (st.getPredicate().equals(DCTERMS.DESCRIPTION)) {	5✔
102	desc = st.getObject().stringValue();	6✔
103	} else if (st.getPredicate().equals(DCTERMS.LICENSE) && st.getObject() instanceof IRI) {	9!
104	license = st.getObject().stringValue();	6✔
105	} else if (st.getPredicate().equals(HAS_SPARQL)) {	5✔
106	// TODO Improve this:
107	queryContent = st.getObject().stringValue().replace("https://w3id.org/np/l/nanopub-query-1.1/repo/", nanopubQueryUrl + "repo/");	10✔
108	} else if (st.getPredicate().equals(HAS_ENDPOINT) && st.getObject() instanceof IRI) {	9!
109	endpoint = st.getObject().stringValue();	5✔
110	if (endpoint.startsWith("https://w3id.org/np/l/nanopub-query-1.1/repo/")) {	5!
111	endpoint = endpoint.replace("https://w3id.org/np/l/nanopub-query-1.1/repo/", nanopubQueryUrl + "repo/");	9✔
112	} else {
113	// TODO Raise exception
114	endpoint = null;	×
115	}
116	}
117	}	1✔
118
119	final Set<String> placeholders = new HashSet<>();	4✔
120	// TODO Make sure we properly handle MalformedQueryException thrown here:
121	ParsedQuery query = new SPARQLParser().parseQuery(queryContent, null);	8✔
122	query.getTupleExpr().visitChildren(new AbstractSimpleQueryModelVisitor<>() {	14✔
123
124	@Override
125	public void meet(Var node) throws RuntimeException {
126	super.meet(node);	3✔
127	if (!node.isConstant() && !node.isAnonymous() && node.getName().startsWith("_")) {	11!
128	placeholders.add(node.getName());	×
129	}
130	}	1✔
131
132	});
133	List<String> placeholdersListPre = new ArrayList<>(placeholders);	5✔
134	Collections.sort(placeholdersListPre);	2✔
135	placeholdersListPre.sort(Comparator.comparing(String::length));	4✔
136	placeholdersList = Collections.unmodifiableList(placeholdersListPre);	4✔
137	}	1✔
138
139	/**
140	* Returns the grlc spec as a string.
141	*
142	* @return grlc specification string
143	*/
144	public String getSpec() {
145	if (np == null) return null;	5✔
146	String s = "";	2✔
147	if (queryPart.isEmpty()) {	4✔
148	if (label == null) {	3!
149	s += "title: \"untitled query\"\n";	×
150	} else {
151	s += "title: \"" + escapeLiteral(label) + "\"\n";	6✔
152	}
153	s += "description: \"" + escapeLiteral(desc) + "\"\n";	6✔
154	StringBuilder userName = new StringBuilder();	4✔
155	Set<IRI> creators = SimpleCreatorPattern.getCreators(np);	4✔
156	for (IRI userIri : creators) {	10✔
157	userName.append(", ").append(userIri);	6✔
158	}	1✔
159	if (!userName.isEmpty()) userName = new StringBuilder(userName.substring(2));	10!
160	String url = "";	2✔
161	if (!creators.isEmpty()) url = creators.iterator().next().stringValue();	9!
162	s += "contact:\n";	3✔
163	s += " name: \"" + escapeLiteral(userName.toString()) + "\"\n";	6✔
164	s += " url: " + url + "\n";	4✔
165	if (license != null) {	3!
166	s += "licence: " + license + "\n";	5✔
167	}
168	s += "queries:\n";	3✔
169	s += " - " + nanopubQueryUrl + requestUrlBase + artifactCode + "/" + queryName + ".rq";	10✔
170	} else if (queryPart.equals(queryName + ".rq")) {	8✔
171	if (label != null) {	3!
172	s += "#+ summary: \"" + escapeLiteral(label) + "\"\n";	6✔
173	}
174	if (desc != null) {	3!
175	s += "#+ description: \"" + escapeLiteral(desc) + "\"\n";	6✔
176	}
177	if (license != null) {	3!
178	s += "#+ licence: " + license + "\n";	5✔
179	}
180	if (endpoint != null) {	3!
181	s += "#+ endpoint: " + endpoint + "\n";	5✔
182	}
183	s += "\n";	3✔
184	s += queryContent;	6✔
185	} else {
186	return null;	2✔
187	}
188	return s;	2✔
189	}
190
191	public String getRepoName() {
192	return endpoint.replaceAll("/", "_").replaceFirst("^.*_repo_", "");	×
193	}
194
195	public String getQueryContent() {
196	return queryContent;	×
197	}
198
199	public String getExpandedQueryContent() {
200	String expanded = queryContent;	×
201	for (String ph : placeholdersList) {	×
202	log.info("ph: ", ph);	×
203	log.info("getParamName(ph): ", getParamName(ph));	×
204	if (isMultiPlaceholder(ph)) {	×
205	// TODO multi placeholders need proper documentation
206	List<String> val = parameters.getAll(getParamName(ph));	×
207	if (!isOptionalPlaceholder(ph) && val.isEmpty()) {	×
208	// TODO throw exception
209	return null;	×
210	}
211	if (val.isEmpty()) {	×
212	expanded = expanded.replaceAll("values\\s\\?" + ph + "\\s\\{\\s\\}(\\s\\.)?", "");	×
213	continue;	×
214	}
215	String valueList = "";	×
216	for (String v : val) {	×
217	if (isIriPlaceholder(ph)) {	×
218	valueList += serializeIri(v) + " ";	×
219	} else {
220	valueList += serializeLiteral(v) + " ";	×
221	}
222	}	×
223	expanded = expanded.replaceAll("values\\s\\?" + ph + "\\s\\{\\s*\\}", "values ?" + ph + " { " + valueList + "}");	×
224	} else {	×
225	String val = parameters.get(getParamName(ph));	×
226	log.info("val: ", val);	×
227	if (!isOptionalPlaceholder(ph) && val == null) {	×
228	// TODO throw exception
229	return null;	×
230	}
231	if (val == null) continue;	×
232	if (isIriPlaceholder(ph)) {	×
233	expanded = expanded.replaceAll("\\?" + ph, serializeIri(val));	×
234	} else {
235	expanded = expanded.replaceAll("\\?" + ph, serializeLiteral(val));	×
236	}
237	}
238	}	×
239	log.info("expanded: ", expanded);	×
240	return expanded;	×
241	}
242
243	public static String escapeLiteral(String s) {
244	return s.replace("\\", "\\\\").replace("\n", "\\n").replace("\"", "\\\"");	11✔
245	}
246
247	public static boolean isOptionalPlaceholder(String placeholder) {
248	return placeholder.startsWith("__");	×
249	}
250
251	public static boolean isMultiPlaceholder(String placeholder) {
252	return placeholder.endsWith("_multi") \|\| placeholder.endsWith("_multi_iri");	×
253	}
254
255	public static boolean isIriPlaceholder(String placeholder) {
256	return placeholder.endsWith("_iri");	×
257	}
258
259	public static String getParamName(String placeholder) {
260	return placeholder.replaceFirst("^_+", "").replaceFirst("_iri$", "").replaceFirst("_multi$", "");	×
261	}
262
263	public static String serializeIri(String iriString) {
264	return "<" + iriString + ">";	×
265	}
266
267	public static String serializeLiteral(String literalString) {
268	return "\"" + escapeLiteral(literalString) + "\"";	×
269	}
270
271	}

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