26363907074

Committed 24 May 2026 02:28PM UTC coverage: 59.543% (+0.8%) from 58.782%

Build # 26363907074

Build Type

Pull #109

github

Committed by

web-flow

Commit Message

Merge c7b82a8e1 into 559f767ae

Pull Request Pull Request #109: refactor(GrlcSpec): delegate to QueryTemplate (nanopub-java 1.89.0)

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68.11

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

package com.knowledgepixels.query;

import io.vertx.core.MultiMap;
import net.trustyuri.TrustyUriUtils;
import org.eclipse.rdf4j.model.IRI;
import org.eclipse.rdf4j.model.vocabulary.DCTERMS;
import org.eclipse.rdf4j.query.QueryLanguage;
import org.eclipse.rdf4j.query.TupleQueryResult;
import org.eclipse.rdf4j.repository.RepositoryConnection;
import org.eclipse.rdf4j.rio.RDFFormat;
import org.nanopub.MalformedNanopubException;
import org.nanopub.Nanopub;
import org.nanopub.NanopubImpl;
import org.nanopub.SimpleCreatorPattern;
import org.nanopub.extra.server.GetNanopub;
import org.nanopub.extra.services.QueryTemplate;
import org.nanopub.vocabulary.NPA;
import org.nanopub.vocabulary.NPX;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import java.io.ByteArrayInputStream;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Base64;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.concurrent.ConcurrentHashMap;

/**
 * Nanopub Query-specific wrapper around {@link QueryTemplate} that adds:
 * <ul>
 *   <li>request-URL parsing ({@code /…/RA…/{name}.rq})</li>
 *   <li>nanopub fetch cache</li>
 *   <li>the {@code _nanopub_trig} inline-nanopub parameter</li>
 *   <li>{@code api-version=latest} resolution against the local meta repo</li>
 *   <li>rewriting the canonical {@code https://w3id.org/np/l/nanopub-query-1.1/repo/}
 *       endpoint prefix to the in-cluster {@code NANOPUB_QUERY_URL/repo/}, plus
 *       validation that the endpoint matches the canonical prefix</li>
 *   <li>{@link #getSpec()} YAML rendering for the legacy {@code /grlc-spec/} route</li>
 *   <li>{@link #getRepoName()} derived from the rewritten endpoint</li>
 * </ul>
 * <p>Parsing, placeholder extraction and SPARQL expansion are delegated to
 * {@link QueryTemplate}. Static placeholder helpers are forwarded so existing
 * callers ({@link OpenApiSpecPage}) keep compiling.
 */
public class GrlcSpec {

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

    private static final ConcurrentHashMap<String, Nanopub> nanopubCache = new ConcurrentHashMap<>();

    /**
     * Exception for invalid grlc specifications.
     */
    public static class InvalidGrlcSpecException extends Exception {

        private InvalidGrlcSpecException(String msg) {
            super(msg);
        }

        private InvalidGrlcSpecException(String msg, Throwable throwable) {
            super(msg, throwable);
        }

    }

    /**
     * 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 static final String NANOPUB_QUERY_REPO_URL = "https://w3id.org/np/l/nanopub-query-1.1/repo/";

    private final MultiMap parameters;
    private final QueryTemplate template;
    private final String requestUrlBase;
    private final String artifactCode;
    private final String queryPart;
    private final String queryContent;
    private final String endpoint;

    /**
     * Creates a new page instance.
     *
     * @param requestUrl The request URL
     * @param parameters The URL request parameters
     */
    public GrlcSpec(String requestUrl, MultiMap parameters) throws InvalidGrlcSpecException {
        this.parameters = parameters;
        requestUrl = requestUrl.replaceFirst("\\?.*$", "");
        if (!requestUrl.matches(".*/RA[A-Za-z0-9\\-_]{43}/(.*)?")) {
            throw new InvalidGrlcSpecException("Invalid grlc API request: " + requestUrl);
        }
        String parsedArtifactCode = requestUrl.replaceFirst("^(.*/)(RA[A-Za-z0-9\\-_]{43})/(.*)?$", "$2");
        requestUrlBase = requestUrl.replaceFirst("^/(.*/)(RA[A-Za-z0-9\\-_]{43})/(.*)?$", "$1");

        String parsedQueryPart = requestUrl.replaceFirst("^(.*/)(RA[A-Za-z0-9\\-_]{43}/)(.*)?$", "$3");
        parsedQueryPart = parsedQueryPart.replaceFirst(".rq$", "");
        queryPart = parsedQueryPart;

        Nanopub np;
        String nanopubParam = parameters.get("_nanopub_trig");
        if (nanopubParam != null && !nanopubParam.isEmpty()) {
            try {
                byte[] trig = Base64.getUrlDecoder().decode(nanopubParam);
                np = new NanopubImpl(new ByteArrayInputStream(trig), RDFFormat.TRIG);
            } catch (MalformedNanopubException | IOException | IllegalArgumentException ex) {
                throw new InvalidGrlcSpecException("Failed to parse nanopub from 'nanopub' parameter", ex);
            }
        } else {
            np = nanopubCache.computeIfAbsent(parsedArtifactCode, GetNanopub::get);
        }
        // TODO rename "api-version" to "_api_version" for consistency
        if (parameters.get("api-version") != null && parameters.get("api-version").equals("latest")) {
            String latestUri = getLatestVersionIdLocally(np.getUri().stringValue());
            if (!latestUri.equals(np.getUri().stringValue())) {
                np = nanopubCache.computeIfAbsent(TrustyUriUtils.getArtifactCode(latestUri), GetNanopub::get);
            }
            parsedArtifactCode = TrustyUriUtils.getArtifactCode(np.getUri().stringValue());
        }
        artifactCode = parsedArtifactCode;

        try {
            if (queryPart.isEmpty()) {
                template = new QueryTemplate(np);
            } else {
                template = new QueryTemplate(np, artifactCode + "/" + queryPart);
            }
        } catch (IllegalArgumentException ex) {
            throw new InvalidGrlcSpecException(ex.getMessage(), ex);
        }

        if (!queryPart.isEmpty() && !queryPart.equals(template.getQuerySuffix())) {
            throw new InvalidGrlcSpecException(
                    "Query part doesn't match query name: " + queryPart + " / " + template.getQuerySuffix());
        }

        queryContent = template.getSparql().replace(NANOPUB_QUERY_REPO_URL, nanopubQueryUrl + "repo/");

        IRI rawEndpoint = template.getEndpoint();
        if (rawEndpoint != null) {
            String ep = rawEndpoint.stringValue();
            if (!ep.startsWith(NANOPUB_QUERY_REPO_URL)) {
                throw new InvalidGrlcSpecException("Invalid/non-recognized endpoint: " + ep);
            }
            endpoint = ep.replace(NANOPUB_QUERY_REPO_URL, nanopubQueryUrl + "repo/");
        } else {
            endpoint = null;
        }
    }

    /**
     * Returns the grlc spec as a string.
     *
     * @return grlc specification string
     */
    public String getSpec() {
        String s = "";
        String label = template.getLabel();
        String desc = template.getDescription();
        IRI license = template.getLicense();
        String queryName = template.getQuerySuffix();
        if (queryPart.isEmpty()) {
            if (label == null) {
                s += "title: \"untitled query\"\n";
            } else {
                s += "title: \"" + QueryTemplate.escapeLiteral(label) + "\"\n";
            }
            s += "description: \"" + QueryTemplate.escapeLiteral(desc) + "\"\n";
            StringBuilder userName = new StringBuilder();
            Set<IRI> creators = SimpleCreatorPattern.getCreators(template.getNanopub());
            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: \"" + QueryTemplate.escapeLiteral(userName.toString()) + "\"\n";
            s += "  url: " + url + "\n";
            if (license != null) {
                s += "licence: " + license.stringValue() + "\n";
            }
            s += "queries:\n";
            s += "  - " + nanopubQueryUrl + requestUrlBase + artifactCode + "/" + queryName + ".rq";
        } else if (queryPart.equals(queryName)) {
            if (label != null) {
                s += "#+ summary: \"" + QueryTemplate.escapeLiteral(label) + "\"\n";
            }
            if (desc != null) {
                s += "#+ description: \"" + QueryTemplate.escapeLiteral(desc) + "\"\n";
            }
            if (license != null) {
                s += "#+ licence: " + license.stringValue() + "\n";
            }
            if (endpoint != null) {
                s += "#+ endpoint: " + endpoint + "\n";
            }
            s += "\n";
            s += queryContent;
        } else {
            throw new RuntimeException("Unexpected queryPart: " + queryPart);
        }
        return s;
    }

    /**
     * Returns the request parameters.
     *
     * @return the request parameters
     */
    public MultiMap getParameters() {
        return parameters;
    }

    /**
     * Returns the nanopub.
     *
     * @return the nanopub
     */
    public Nanopub getNanopub() {
        return template.getNanopub();
    }

    /**
     * Returns the artifact code.
     *
     * @return the artifact code
     */
    public String getArtifactCode() {
        return artifactCode;
    }

    /**
     * Returns the label.
     *
     * @return the label
     */
    public String getLabel() {
        return template.getLabel();
    }

    /**
     * Returns the description.
     *
     * @return the description
     */
    public String getDescription() {
        return template.getDescription();
    }

    /**
     * Returns the query name.
     *
     * @return the query name
     */
    public String getQueryName() {
        return template.getQuerySuffix();
    }

    /**
     * Returns the list of placeholders.
     *
     * @return the list of placeholders
     */
    public List<String> getPlaceholdersList() {
        return template.getPlaceholdersList();
    }

    /**
     * Returns the repository name derived from the endpoint URL.
     *
     * @return the repository name
     */
    public String getRepoName() {
        return endpoint.replaceAll("/", "_").replaceFirst("^.*_repo_", "");
    }

    /**
     * Returns the query content (with the canonical repo URL rewritten to the
     * in-cluster {@link #nanopubQueryUrl}{@code /repo/}).
     *
     * @return the query content
     */
    public String getQueryContent() {
        return queryContent;
    }

    public boolean isConstructQuery() {
        return template.isConstructQuery();
    }

    /**
     * Expands the query by replacing the placeholders with the provided parameter
     * values, and rewrites the canonical repo URL to the in-cluster one.
     *
     * @return the expanded query
     * @throws InvalidGrlcSpecException if a non-optional placeholder is missing a value
     */
    public String expandQuery() throws InvalidGrlcSpecException {
        Map<String, List<String>> params = new LinkedHashMap<>();
        for (String name : parameters.names()) {
            params.put(name, new ArrayList<>(parameters.getAll(name)));
        }
        logger.info("Expanding grlc query with parameters: {}", parameters);
        try {
            String expanded = template.expandQuery(params);
            return expanded.replace(NANOPUB_QUERY_REPO_URL, nanopubQueryUrl + "repo/");
        } catch (IllegalArgumentException ex) {
            throw new InvalidGrlcSpecException(ex.getMessage(), ex);
        }
    }

    /**
     * Escapes a literal string for SPARQL.
     *
     * @param s The string
     * @return The escaped string
     */
    public static String escapeLiteral(String s) {
        return QueryTemplate.escapeLiteral(s);
    }

    /**
     * Checks whether the given placeholder is an optional placeholder.
     *
     * @param placeholder The placeholder name
     * @return true if it is an optional placeholder, false otherwise
     */
    public static boolean isOptionalPlaceholder(String placeholder) {
        return QueryTemplate.isOptionalPlaceholder(placeholder);
    }

    /**
     * Checks whether the given placeholder is a multi-value placeholder.
     *
     * @param placeholder The placeholder name
     * @return true if it is a multi-value placeholder, false otherwise
     */
    public static boolean isMultiPlaceholder(String placeholder) {
        return QueryTemplate.isMultiPlaceholder(placeholder);
    }

    /**
     * Checks whether the given placeholder is an IRI placeholder.
     *
     * @param placeholder The placeholder name
     * @return true if it is an IRI placeholder, false otherwise
     */
    public static boolean isIriPlaceholder(String placeholder) {
        return QueryTemplate.isIriPlaceholder(placeholder);
    }

    /**
     * Returns the parameter name for the given placeholder.
     *
     * @param placeholder The placeholder name
     * @return The parameter name
     */
    public static String getParamName(String placeholder) {
        return QueryTemplate.getParamName(placeholder);
    }

    /**
     * Serializes an IRI string for SPARQL.
     *
     * @param iriString The IRI string
     * @return The serialized IRI
     */
    public static String serializeIri(String iriString) {
        return QueryTemplate.serializeIri(iriString);
    }

    /**
     * Serializes a literal string for SPARQL.
     *
     * @param literalString The literal string
     * @return The serialized literal
     */
    public static String serializeLiteral(String literalString) {
        return QueryTemplate.serializeLiteral(literalString);
    }

    /**
     * Resolves the latest version of a nanopub by following the supersedes chain in the local store.
     * Uses a single SPARQL query with a property path to find the latest non-invalidated version
     * signed by the same key. If no result is found locally, or if the local store is unavailable,
     * returns the original URI.
     *
     * @param nanopubUri the URI of the nanopub to resolve
     * @return the URI of the latest version
     */
    static String getLatestVersionIdLocally(String nanopubUri) {
        logger.info("Resolving latest version locally for: {}", nanopubUri);
        try {
            RepositoryConnection conn = TripleStore.get().getRepoConnection("meta");
            try (conn) {
                String query =
                        "SELECT ?latest ?date WHERE { " +
                        "GRAPH <" + NPA.GRAPH + "> { " +
                        "<" + nanopubUri + "> <" + NPA.HAS_VALID_SIGNATURE_FOR_PUBLIC_KEY + "> ?pubkey . " +
                        "?latest <" + NPA.HAS_VALID_SIGNATURE_FOR_PUBLIC_KEY + "> ?pubkey . " +
                        "FILTER NOT EXISTS { ?npx <" + NPX.INVALIDATES + "> ?latest ; " +
                        "<" + NPA.HAS_VALID_SIGNATURE_FOR_PUBLIC_KEY + "> ?pubkey . } " +
                        "?latest <" + DCTERMS.CREATED + "> ?date . " +
                        "} " +
                        "GRAPH <" + NPA.NETWORK_GRAPH + "> { " +
                        "?latest (<" + NPX.SUPERSEDES + ">)* <" + nanopubUri + "> . " +
                        "} " +
                        "} ORDER BY DESC(?date) LIMIT 1";
                TupleQueryResult r = conn.prepareTupleQuery(QueryLanguage.SPARQL, query).evaluate();
                try (r) {
                    if (r.hasNext()) {
                        String latestUri = r.next().getBinding("latest").getValue().stringValue();
                        logger.info("Resolved latest version: {}", latestUri);
                        return latestUri;
                    }
                }
                logger.info("No latest version found locally for: {}", nanopubUri);
                return nanopubUri;
            }
        } catch (Exception ex) {
            logger.warn("Could not resolve latest version locally, using original version: {}", ex.getMessage());
            return nanopubUri;
        }
    }

}

1	package com.knowledgepixels.query;
2
3	import io.vertx.core.MultiMap;
4	import net.trustyuri.TrustyUriUtils;
5	import org.eclipse.rdf4j.model.IRI;
6	import org.eclipse.rdf4j.model.vocabulary.DCTERMS;
7	import org.eclipse.rdf4j.query.QueryLanguage;
8	import org.eclipse.rdf4j.query.TupleQueryResult;
9	import org.eclipse.rdf4j.repository.RepositoryConnection;
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.SimpleCreatorPattern;
15	import org.nanopub.extra.server.GetNanopub;
16	import org.nanopub.extra.services.QueryTemplate;
17	import org.nanopub.vocabulary.NPA;
18	import org.nanopub.vocabulary.NPX;
19	import org.slf4j.Logger;
20	import org.slf4j.LoggerFactory;
21
22	import java.io.ByteArrayInputStream;
23	import java.io.IOException;
24	import java.util.ArrayList;
25	import java.util.Base64;
26	import java.util.LinkedHashMap;
27	import java.util.List;
28	import java.util.Map;
29	import java.util.Set;
30	import java.util.concurrent.ConcurrentHashMap;
31
32	/**
33	* Nanopub Query-specific wrapper around {@link QueryTemplate} that adds:
34	* <ul>
35	* <li>request-URL parsing ({@code /…/RA…/{name}.rq})</li>
36	* <li>nanopub fetch cache</li>
37	* <li>the {@code _nanopub_trig} inline-nanopub parameter</li>
38	* <li>{@code api-version=latest} resolution against the local meta repo</li>
39	* <li>rewriting the canonical {@code https://w3id.org/np/l/nanopub-query-1.1/repo/}
40	* endpoint prefix to the in-cluster {@code NANOPUB_QUERY_URL/repo/}, plus
41	* validation that the endpoint matches the canonical prefix</li>
42	* <li>{@link #getSpec()} YAML rendering for the legacy {@code /grlc-spec/} route</li>
43	* <li>{@link #getRepoName()} derived from the rewritten endpoint</li>
44	* </ul>
45	* <p>Parsing, placeholder extraction and SPARQL expansion are delegated to
46	* {@link QueryTemplate}. Static placeholder helpers are forwarded so existing
47	* callers ({@link OpenApiSpecPage}) keep compiling.
48	*/
49	public class GrlcSpec {
50
51	private static final Logger logger = LoggerFactory.getLogger(GrlcSpec.class);	9✔
52
53	private static final ConcurrentHashMap<String, Nanopub> nanopubCache = new ConcurrentHashMap<>();	12✔
54
55	/**
56	* Exception for invalid grlc specifications.
57	*/
58	public static class InvalidGrlcSpecException extends Exception {
59
60	private InvalidGrlcSpecException(String msg) {
61	super(msg);	9✔
62	}	3✔
63
64	private InvalidGrlcSpecException(String msg, Throwable throwable) {
65	super(msg, throwable);	12✔
66	}	3✔
67
68	}
69
70	/**
71	* URL for the given Nanopub Query instance, needed for internal coordination.
72	*/
73	public static final String nanopubQueryUrl = Utils.getEnvString("NANOPUB_QUERY_URL", "http://query:9393/");	15✔
74
75	private static final String NANOPUB_QUERY_REPO_URL = "https://w3id.org/np/l/nanopub-query-1.1/repo/";
76
77	private final MultiMap parameters;
78	private final QueryTemplate template;
79	private final String requestUrlBase;
80	private final String artifactCode;
81	private final String queryPart;
82	private final String queryContent;
83	private final String endpoint;
84
85	/**
86	* Creates a new page instance.
87	*
88	* @param requestUrl The request URL
89	* @param parameters The URL request parameters
90	*/
91	public GrlcSpec(String requestUrl, MultiMap parameters) throws InvalidGrlcSpecException {	6✔
92	this.parameters = parameters;	9✔
93	requestUrl = requestUrl.replaceFirst("\\?.*$", "");	15✔
94	if (!requestUrl.matches("./RA[A-Za-z0-9\\-_]{43}/(.)?")) {	12✔
95	throw new InvalidGrlcSpecException("Invalid grlc API request: " + requestUrl);	18✔
96	}
97	String parsedArtifactCode = requestUrl.replaceFirst("^(./)(RA[A-Za-z0-9\\-_]{43})/(.)?$", "$2");	15✔
98	requestUrlBase = requestUrl.replaceFirst("^/(./)(RA[A-Za-z0-9\\-_]{43})/(.)?$", "$1");	18✔
99
100	String parsedQueryPart = requestUrl.replaceFirst("^(./)(RA[A-Za-z0-9\\-_]{43}/)(.)?$", "$3");	15✔
101	parsedQueryPart = parsedQueryPart.replaceFirst(".rq$", "");	15✔
102	queryPart = parsedQueryPart;	9✔
103
104	Nanopub np;
105	String nanopubParam = parameters.get("_nanopub_trig");	12✔
106	if (nanopubParam != null && !nanopubParam.isEmpty()) {	6!
107	try {
108	byte[] trig = Base64.getUrlDecoder().decode(nanopubParam);	×
109	np = new NanopubImpl(new ByteArrayInputStream(trig), RDFFormat.TRIG);	×
110	} catch (MalformedNanopubException \| IOException \| IllegalArgumentException ex) {	×
111	throw new InvalidGrlcSpecException("Failed to parse nanopub from 'nanopub' parameter", ex);	×
112	}	×
113	} else {
114	np = nanopubCache.computeIfAbsent(parsedArtifactCode, GetNanopub::get);	18✔
115	}
116	// TODO rename "api-version" to "_api_version" for consistency
117	if (parameters.get("api-version") != null && parameters.get("api-version").equals("latest")) {	30✔
118	String latestUri = getLatestVersionIdLocally(np.getUri().stringValue());	15✔
119	if (!latestUri.equals(np.getUri().stringValue())) {	18!
120	np = nanopubCache.computeIfAbsent(TrustyUriUtils.getArtifactCode(latestUri), GetNanopub::get);	×
121	}
122	parsedArtifactCode = TrustyUriUtils.getArtifactCode(np.getUri().stringValue());	15✔
123	}
124	artifactCode = parsedArtifactCode;	9✔
125
126	try {
127	if (queryPart.isEmpty()) {	12✔
128	template = new QueryTemplate(np);	21✔
129	} else {
130	template = new QueryTemplate(np, artifactCode + "/" + queryPart);	33✔
131	}
132	} catch (IllegalArgumentException ex) {	3✔
133	throw new InvalidGrlcSpecException(ex.getMessage(), ex);	21✔
134	}	3✔
135
136	if (!queryPart.isEmpty() && !queryPart.equals(template.getQuerySuffix())) {	33!
137	throw new InvalidGrlcSpecException(	×
138	"Query part doesn't match query name: " + queryPart + " / " + template.getQuerySuffix());	×
139	}
140
141	queryContent = template.getSparql().replace(NANOPUB_QUERY_REPO_URL, nanopubQueryUrl + "repo/");	27✔
142
143	IRI rawEndpoint = template.getEndpoint();	12✔
144	if (rawEndpoint != null) {	6!
145	String ep = rawEndpoint.stringValue();	9✔
146	if (!ep.startsWith(NANOPUB_QUERY_REPO_URL)) {	12!
147	throw new InvalidGrlcSpecException("Invalid/non-recognized endpoint: " + ep);	×
148	}
149	endpoint = ep.replace(NANOPUB_QUERY_REPO_URL, nanopubQueryUrl + "repo/");	21✔
150	} else {	3✔
151	endpoint = null;	×
152	}
153	}	3✔
154
155	/**
156	* Returns the grlc spec as a string.
157	*
158	* @return grlc specification string
159	*/
160	public String getSpec() {
161	String s = "";	6✔
162	String label = template.getLabel();	12✔
163	String desc = template.getDescription();	12✔
164	IRI license = template.getLicense();	12✔
165	String queryName = template.getQuerySuffix();	12✔
166	if (queryPart.isEmpty()) {	12✔
167	if (label == null) {	6!
168	s += "title: \"untitled query\"\n";	×
169	} else {
170	s += "title: \"" + QueryTemplate.escapeLiteral(label) + "\"\n";	15✔
171	}
172	s += "description: \"" + QueryTemplate.escapeLiteral(desc) + "\"\n";	15✔
173	StringBuilder userName = new StringBuilder();	12✔
174	Set<IRI> creators = SimpleCreatorPattern.getCreators(template.getNanopub());	15✔
175	for (IRI userIri : creators) {	30✔
176	userName.append(", ").append(userIri);	18✔
177	}	3✔
178	if (!userName.isEmpty()) {	9!
179	userName = new StringBuilder(userName.substring(2));	21✔
180	}
181	String url = "";	6✔
182	if (!creators.isEmpty()) {	9!
183	url = creators.iterator().next().stringValue();	18✔
184	}
185	s += "contact:\n";	9✔
186	s += " name: \"" + QueryTemplate.escapeLiteral(userName.toString()) + "\"\n";	18✔
187	s += " url: " + url + "\n";	12✔
188	if (license != null) {	6!
189	s += "licence: " + license.stringValue() + "\n";	15✔
190	}
191	s += "queries:\n";	9✔
192	s += " - " + nanopubQueryUrl + requestUrlBase + artifactCode + "/" + queryName + ".rq";	27✔
193	} else if (queryPart.equals(queryName)) {	18!
194	if (label != null) {	6!
195	s += "#+ summary: \"" + QueryTemplate.escapeLiteral(label) + "\"\n";	15✔
196	}
197	if (desc != null) {	6!
198	s += "#+ description: \"" + QueryTemplate.escapeLiteral(desc) + "\"\n";	15✔
199	}
200	if (license != null) {	6!
201	s += "#+ licence: " + license.stringValue() + "\n";	15✔
202	}
203	if (endpoint != null) {	9!
204	s += "#+ endpoint: " + endpoint + "\n";	15✔
205	}
206	s += "\n";	9✔
207	s += queryContent;	18✔
208	} else {
209	throw new RuntimeException("Unexpected queryPart: " + queryPart);	×
210	}
211	return s;	6✔
212	}
213
214	/**
215	* Returns the request parameters.
216	*
217	* @return the request parameters
218	*/
219	public MultiMap getParameters() {
220	return parameters;	9✔
221	}
222
223	/**
224	* Returns the nanopub.
225	*
226	* @return the nanopub
227	*/
228	public Nanopub getNanopub() {
229	return template.getNanopub();	12✔
230	}
231
232	/**
233	* Returns the artifact code.
234	*
235	* @return the artifact code
236	*/
237	public String getArtifactCode() {
238	return artifactCode;	9✔
239	}
240
241	/**
242	* Returns the label.
243	*
244	* @return the label
245	*/
246	public String getLabel() {
247	return template.getLabel();	12✔
248	}
249
250	/**
251	* Returns the description.
252	*
253	* @return the description
254	*/
255	public String getDescription() {
256	return template.getDescription();	12✔
257	}
258
259	/**
260	* Returns the query name.
261	*
262	* @return the query name
263	*/
264	public String getQueryName() {
265	return template.getQuerySuffix();	12✔
266	}
267
268	/**
269	* Returns the list of placeholders.
270	*
271	* @return the list of placeholders
272	*/
273	public List<String> getPlaceholdersList() {
274	return template.getPlaceholdersList();	12✔
275	}
276
277	/**
278	* Returns the repository name derived from the endpoint URL.
279	*
280	* @return the repository name
281	*/
282	public String getRepoName() {
283	return endpoint.replaceAll("/", "_").replaceFirst("^.*_repo_", "");	27✔
284	}
285
286	/**
287	* Returns the query content (with the canonical repo URL rewritten to the
288	* in-cluster {@link #nanopubQueryUrl}{@code /repo/}).
289	*
290	* @return the query content
291	*/
292	public String getQueryContent() {
293	return queryContent;	9✔
294	}
295
296	public boolean isConstructQuery() {
297	return template.isConstructQuery();	12✔
298	}
299
300	/**
301	* Expands the query by replacing the placeholders with the provided parameter
302	* values, and rewrites the canonical repo URL to the in-cluster one.
303	*
304	* @return the expanded query
305	* @throws InvalidGrlcSpecException if a non-optional placeholder is missing a value
306	*/
307	public String expandQuery() throws InvalidGrlcSpecException {
308	Map<String, List<String>> params = new LinkedHashMap<>();	×
309	for (String name : parameters.names()) {	×
310	params.put(name, new ArrayList<>(parameters.getAll(name)));	×
311	}	×
312	logger.info("Expanding grlc query with parameters: {}", parameters);	×
313	try {
314	String expanded = template.expandQuery(params);	×
315	return expanded.replace(NANOPUB_QUERY_REPO_URL, nanopubQueryUrl + "repo/");	×
316	} catch (IllegalArgumentException ex) {	×
317	throw new InvalidGrlcSpecException(ex.getMessage(), ex);	×
318	}
319	}
320
321	/**
322	* Escapes a literal string for SPARQL.
323	*
324	* @param s The string
325	* @return The escaped string
326	*/
327	public static String escapeLiteral(String s) {
328	return QueryTemplate.escapeLiteral(s);	×
329	}
330
331	/**
332	* Checks whether the given placeholder is an optional placeholder.
333	*
334	* @param placeholder The placeholder name
335	* @return true if it is an optional placeholder, false otherwise
336	*/
337	public static boolean isOptionalPlaceholder(String placeholder) {
338	return QueryTemplate.isOptionalPlaceholder(placeholder);	9✔
339	}
340
341	/**
342	* Checks whether the given placeholder is a multi-value placeholder.
343	*
344	* @param placeholder The placeholder name
345	* @return true if it is a multi-value placeholder, false otherwise
346	*/
347	public static boolean isMultiPlaceholder(String placeholder) {
348	return QueryTemplate.isMultiPlaceholder(placeholder);	9✔
349	}
350
351	/**
352	* Checks whether the given placeholder is an IRI placeholder.
353	*
354	* @param placeholder The placeholder name
355	* @return true if it is an IRI placeholder, false otherwise
356	*/
357	public static boolean isIriPlaceholder(String placeholder) {
358	return QueryTemplate.isIriPlaceholder(placeholder);	9✔
359	}
360
361	/**
362	* Returns the parameter name for the given placeholder.
363	*
364	* @param placeholder The placeholder name
365	* @return The parameter name
366	*/
367	public static String getParamName(String placeholder) {
368	return QueryTemplate.getParamName(placeholder);	9✔
369	}
370
371	/**
372	* Serializes an IRI string for SPARQL.
373	*
374	* @param iriString The IRI string
375	* @return The serialized IRI
376	*/
377	public static String serializeIri(String iriString) {
378	return QueryTemplate.serializeIri(iriString);	9✔
379	}
380
381	/**
382	* Serializes a literal string for SPARQL.
383	*
384	* @param literalString The literal string
385	* @return The serialized literal
386	*/
387	public static String serializeLiteral(String literalString) {
388	return QueryTemplate.serializeLiteral(literalString);	9✔
389	}
390
391	/**
392	* Resolves the latest version of a nanopub by following the supersedes chain in the local store.
393	* Uses a single SPARQL query with a property path to find the latest non-invalidated version
394	* signed by the same key. If no result is found locally, or if the local store is unavailable,
395	* returns the original URI.
396	*
397	* @param nanopubUri the URI of the nanopub to resolve
398	* @return the URI of the latest version
399	*/
400	static String getLatestVersionIdLocally(String nanopubUri) {
401	logger.info("Resolving latest version locally for: {}", nanopubUri);	12✔
402	try {
403	RepositoryConnection conn = TripleStore.get().getRepoConnection("meta");	×
404	try (conn) {	×
405	String query =	×
406	"SELECT ?latest ?date WHERE { " +
407	"GRAPH <" + NPA.GRAPH + "> { " +
408	"<" + nanopubUri + "> <" + NPA.HAS_VALID_SIGNATURE_FOR_PUBLIC_KEY + "> ?pubkey . " +
409	"?latest <" + NPA.HAS_VALID_SIGNATURE_FOR_PUBLIC_KEY + "> ?pubkey . " +
410	"FILTER NOT EXISTS { ?npx <" + NPX.INVALIDATES + "> ?latest ; " +
411	"<" + NPA.HAS_VALID_SIGNATURE_FOR_PUBLIC_KEY + "> ?pubkey . } " +
412	"?latest <" + DCTERMS.CREATED + "> ?date . " +
413	"} " +
414	"GRAPH <" + NPA.NETWORK_GRAPH + "> { " +
415	"?latest (<" + NPX.SUPERSEDES + ">)* <" + nanopubUri + "> . " +
416	"} " +
417	"} ORDER BY DESC(?date) LIMIT 1";
418	TupleQueryResult r = conn.prepareTupleQuery(QueryLanguage.SPARQL, query).evaluate();	×
419	try (r) {	×
420	if (r.hasNext()) {	×
421	String latestUri = r.next().getBinding("latest").getValue().stringValue();	×
422	logger.info("Resolved latest version: {}", latestUri);	×
423	return latestUri;	×
424	}
425	}	×
426	logger.info("No latest version found locally for: {}", nanopubUri);	×
427	return nanopubUri;	×
428	}	×
429	} catch (Exception ex) {	3✔
430	logger.warn("Could not resolve latest version locally, using original version: {}", ex.getMessage());	15✔
431	return nanopubUri;	6✔
432	}
433	}
434
435	}

knowledgepixels / nanopub-query / 26363907074

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