23233444105

Committed 18 Mar 2026 07:16AM UTC coverage: 69.473% (-0.1%) from 69.573%

Build # 23233444105

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github

Committed by

ashleycaselli

Commit Message

chore(vocabulary): add KPXL_GRLC class for GRLC vocabulary IRIs and update references in GrlcSpec

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61.24

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

package com.knowledgepixels.query;

import com.knowledgepixels.query.vocabulary.KPXL_GRLC;
import io.vertx.core.MultiMap;
import net.trustyuri.TrustyUriUtils;
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.MalformedQueryException;
import org.eclipse.rdf4j.query.QueryLanguage;
import org.eclipse.rdf4j.query.TupleQueryResult;
import org.eclipse.rdf4j.query.algebra.Var;
import org.eclipse.rdf4j.query.algebra.helpers.AbstractSimpleQueryModelVisitor;
import org.eclipse.rdf4j.query.parser.ParsedGraphQuery;
import org.eclipse.rdf4j.query.parser.ParsedQuery;
import org.eclipse.rdf4j.query.parser.sparql.SPARQLParser;
import org.eclipse.rdf4j.repository.RepositoryConnection;
import org.nanopub.Nanopub;
import org.nanopub.SimpleCreatorPattern;
import org.nanopub.extra.server.GetNanopub;
import org.nanopub.vocabulary.NPA;
import org.nanopub.vocabulary.NPX;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import java.util.*;

//TODO merge this class with GrlcQuery of Nanodash and move to a library like nanopub-java

/**
 * 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 logger = LoggerFactory.getLogger(GrlcSpec.class);

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

    /**
     * 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("\\?.*$", "");
        if (!requestUrl.matches(".*/RA[A-Za-z0-9\\-_]{43}/(.*)?")) {
            throw new InvalidGrlcSpecException("Invalid grlc API request: " + requestUrl);
        }
        artifactCode = requestUrl.replaceFirst("^(.*/)(RA[A-Za-z0-9\\-_]{43})/(.*)?$", "$2");
        requestUrlBase = requestUrl.replaceFirst("^/(.*/)(RA[A-Za-z0-9\\-_]{43})/(.*)?$", "$1");

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

        // TODO Get the nanopub from the local store:
        np = GetNanopub.get(artifactCode);
        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 = GetNanopub.get(TrustyUriUtils.getArtifactCode(latestUri));
            }
            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)) {
                throw new InvalidGrlcSpecException("Subject suffixes don't match: " + queryName);
            }
            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(KPXL_GRLC.SPARQL)) {
                // TODO Improve this:
                queryContent = st.getObject().stringValue().replace(NANOPUB_QUERY_REPO_URL, nanopubQueryUrl + "repo/");
            } else if (st.getPredicate().equals(KPXL_GRLC.ENDPOINT) && st.getObject() instanceof IRI) {
                endpoint = st.getObject().stringValue();
                if (endpoint.startsWith(NANOPUB_QUERY_REPO_URL)) {
                    endpoint = endpoint.replace(NANOPUB_QUERY_REPO_URL, nanopubQueryUrl + "repo/");
                } else {
                    throw new InvalidGrlcSpecException("Invalid/non-recognized endpoint: " + endpoint);
                }
            }
        }

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

        final Set<String> placeholders = new HashSet<>();
        try {
            ParsedQuery query = new SPARQLParser().parseQuery(queryContent, null);
            isConstructQuery = query instanceof ParsedGraphQuery;
            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());
                    }
                }

            });
        } catch (MalformedQueryException ex) {
            throw new InvalidGrlcSpecException("Invalid SPARQL string", ex);
        }
        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() {
        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)) {
            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 {
            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 np;
    }

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

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

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

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

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

    /**
     * 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.
     *
     * @return the query content
     */
    public String getQueryContent() {
        return queryContent;
    }

    public boolean isConstructQuery() {
        return isConstructQuery;
    }

    /**
     * Expands the query by replacing the placeholders with the provided parameter values.
     *
     * @return the expanded query
     * @throws InvalidGrlcSpecException if a non-optional placeholder is missing a value
     */
    public String expandQuery() throws InvalidGrlcSpecException {
        String expandedQueryContent = queryContent;
        logger.info("Expanding grlc query with parameters: {}", parameters);
        for (String ph : placeholdersList) {
            logger.info("Processing placeholder <{}> associated to parameter with name <{}>", ph, getParamName(ph));
            if (isMultiPlaceholder(ph)) {
                // TODO multi placeholders need proper documentation
                List<String> val = parameters.getAll(getParamName(ph));
                if (!isOptionalPlaceholder(ph) && val.isEmpty()) {
                    throw new InvalidGrlcSpecException("Missing value for non-optional placeholder: " + ph);
                }
                if (val.isEmpty()) {
                    expandedQueryContent = expandedQueryContent.replaceAll("values\\s*\\?" + ph + "\\s*\\{\\s*\\}(\\s*\\.)?", "");
                    continue;
                }
                String valueList = "";
                for (String v : val) {
                    if (isIriPlaceholder(ph)) {
                        valueList += serializeIri(v) + " ";
                    } else {
                        valueList += serializeLiteral(v) + " ";
                    }
                }
                expandedQueryContent = expandedQueryContent.replaceAll("values\\s*\\?" + ph + "\\s*\\{\\s*\\}", "values ?" + ph + " { " + escapeSlashes(valueList) + "}");
            } else {
                String val = parameters.get(getParamName(ph));
                logger.info("Value for placeholder <{}>: {}", ph, val);
                if (!isOptionalPlaceholder(ph) && val == null) {
                    throw new InvalidGrlcSpecException("Missing value for non-optional placeholder: " + ph);
                }
                if (val == null) {
                    continue;
                }
                if (isIriPlaceholder(ph)) {
                    expandedQueryContent = expandedQueryContent.replaceAll("\\?" + ph, escapeSlashes(serializeIri(val)));
                } else {
                    expandedQueryContent = expandedQueryContent.replaceAll("\\?" + ph, escapeSlashes(serializeLiteral(val)));
                }
            }
        }
        return expandedQueryContent;
    }

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

    /**
     * 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 placeholder.startsWith("__");
    }

    /**
     * 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 placeholder.endsWith("_multi") || placeholder.endsWith("_multi_iri");
    }

    /**
     * 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 placeholder.endsWith("_iri");
    }

    /**
     * Returns the parameter name for the given placeholder.
     *
     * @param placeholder The placeholder name
     * @return The parameter name
     */
    public static String getParamName(String placeholder) {
        return placeholder.replaceFirst("^_+", "").replaceFirst("_iri$", "").replaceFirst("_multi$", "");
    }

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

    /**
     * Escapes slashes in a string.
     *
     * @param string The string
     * @return The escaped string
     */
    private static String escapeSlashes(String string) {
        return string.replace("\\", "\\\\");
    }

    /**
     * Serializes a literal string for SPARQL.
     *
     * @param literalString The literal string
     * @return The serialized literal
     */
    public static String serializeLiteral(String literalString) {
        return "\"" + escapeLiteral(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 com.knowledgepixels.query.vocabulary.KPXL_GRLC;
4	import io.vertx.core.MultiMap;
5	import net.trustyuri.TrustyUriUtils;
6	import org.eclipse.rdf4j.model.IRI;
7	import org.eclipse.rdf4j.model.Statement;
8	import org.eclipse.rdf4j.model.ValueFactory;
9	import org.eclipse.rdf4j.model.impl.SimpleValueFactory;
10	import org.eclipse.rdf4j.model.vocabulary.DCTERMS;
11	import org.eclipse.rdf4j.model.vocabulary.RDFS;
12	import org.eclipse.rdf4j.query.MalformedQueryException;
13	import org.eclipse.rdf4j.query.QueryLanguage;
14	import org.eclipse.rdf4j.query.TupleQueryResult;
15	import org.eclipse.rdf4j.query.algebra.Var;
16	import org.eclipse.rdf4j.query.algebra.helpers.AbstractSimpleQueryModelVisitor;
17	import org.eclipse.rdf4j.query.parser.ParsedGraphQuery;
18	import org.eclipse.rdf4j.query.parser.ParsedQuery;
19	import org.eclipse.rdf4j.query.parser.sparql.SPARQLParser;
20	import org.eclipse.rdf4j.repository.RepositoryConnection;
21	import org.nanopub.Nanopub;
22	import org.nanopub.SimpleCreatorPattern;
23	import org.nanopub.extra.server.GetNanopub;
24	import org.nanopub.vocabulary.NPA;
25	import org.nanopub.vocabulary.NPX;
26	import org.slf4j.Logger;
27	import org.slf4j.LoggerFactory;
28
29	import java.util.*;
30
31	//TODO merge this class with GrlcQuery of Nanodash and move to a library like nanopub-java
32
33	/**
34	* This class produces a page with the grlc specification. This is needed internally to tell grlc
35	* how to execute a particular query template.
36	*/
37	public class GrlcSpec {
38
39	private static final ValueFactory vf = SimpleValueFactory.getInstance();	6✔
40
41	private static final Logger logger = LoggerFactory.getLogger(GrlcSpec.class);	9✔
42
43	/**
44	* Exception for invalid grlc specifications.
45	*/
46	public static class InvalidGrlcSpecException extends Exception {
47
48	private InvalidGrlcSpecException(String msg) {
49	super(msg);	9✔
50	}	3✔
51
52	private InvalidGrlcSpecException(String msg, Throwable throwable) {
53	super(msg, throwable);	×
54	}	×
55
56	}
57
58	/**
59	* URL for the given Nanopub Query instance, needed for internal coordination.
60	*/
61	public static final String nanopubQueryUrl = Utils.getEnvString("NANOPUB_QUERY_URL", "http://query:9393/");	15✔
62
63	private static final String NANOPUB_QUERY_REPO_URL = "https://w3id.org/np/l/nanopub-query-1.1/repo/";
64
65	private MultiMap parameters;
66	private Nanopub np;
67	private String requestUrlBase;
68	private String artifactCode;
69	private String queryPart;
70	private String queryName;
71	private String label;
72	private String desc;
73	private String license;
74	private String queryContent;
75	private String endpoint;
76	private List<String> placeholdersList;
77	private boolean isConstructQuery;
78
79	/**
80	* Creates a new page instance.
81	*
82	* @param requestUrl The request URL
83	* @param parameters The URL request parameters
84	*/
85	public GrlcSpec(String requestUrl, MultiMap parameters) throws InvalidGrlcSpecException {	6✔
86	this.parameters = parameters;	9✔
87	requestUrl = requestUrl.replaceFirst("\\?.*$", "");	15✔
88	if (!requestUrl.matches("./RA[A-Za-z0-9\\-_]{43}/(.)?")) {	12✔
89	throw new InvalidGrlcSpecException("Invalid grlc API request: " + requestUrl);	18✔
90	}
91	artifactCode = requestUrl.replaceFirst("^(./)(RA[A-Za-z0-9\\-_]{43})/(.)?$", "$2");	18✔
92	requestUrlBase = requestUrl.replaceFirst("^/(./)(RA[A-Za-z0-9\\-_]{43})/(.)?$", "$1");	18✔
93
94	queryPart = requestUrl.replaceFirst("^(./)(RA[A-Za-z0-9\\-_]{43}/)(.)?$", "$3");	18✔
95	queryPart = queryPart.replaceFirst(".rq$", "");	21✔
96
97	// TODO Get the nanopub from the local store:
98	np = GetNanopub.get(artifactCode);	15✔
99	if (parameters.get("api-version") != null && parameters.get("api-version").equals("latest")) {	30✔
100	String latestUri = getLatestVersionIdLocally(np.getUri().stringValue());	18✔
101	if (!latestUri.equals(np.getUri().stringValue())) {	21!
102	np = GetNanopub.get(TrustyUriUtils.getArtifactCode(latestUri));	×
103	}
104	artifactCode = TrustyUriUtils.getArtifactCode(np.getUri().stringValue());	21✔
105	}
106	for (Statement st : np.getAssertion()) {	36✔
107	if (!st.getSubject().stringValue().startsWith(np.getUri().stringValue())) {	27!
108	continue;	×
109	}
110	String qn = st.getSubject().stringValue().replaceFirst("^.[#/](.)$", "$1");	21✔
111	if (queryName != null && !qn.equals(queryName)) {	24!
112	throw new InvalidGrlcSpecException("Subject suffixes don't match: " + queryName);	×
113	}
114	queryName = qn;	9✔
115	if (st.getPredicate().equals(RDFS.LABEL)) {	15✔
116	label = st.getObject().stringValue();	18✔
117	} else if (st.getPredicate().equals(DCTERMS.DESCRIPTION)) {	15✔
118	desc = st.getObject().stringValue();	18✔
119	} else if (st.getPredicate().equals(DCTERMS.LICENSE) && st.getObject() instanceof IRI) {	27!
120	license = st.getObject().stringValue();	18✔
121	} else if (st.getPredicate().equals(KPXL_GRLC.SPARQL)) {	15✔
122	// TODO Improve this:
123	queryContent = st.getObject().stringValue().replace(NANOPUB_QUERY_REPO_URL, nanopubQueryUrl + "repo/");	30✔
124	} else if (st.getPredicate().equals(KPXL_GRLC.ENDPOINT) && st.getObject() instanceof IRI) {	27!
125	endpoint = st.getObject().stringValue();	15✔
126	if (endpoint.startsWith(NANOPUB_QUERY_REPO_URL)) {	15!
127	endpoint = endpoint.replace(NANOPUB_QUERY_REPO_URL, nanopubQueryUrl + "repo/");	27✔
128	} else {
129	throw new InvalidGrlcSpecException("Invalid/non-recognized endpoint: " + endpoint);	×
130	}
131	}
132	}	3✔
133
134	if (!queryPart.isEmpty() && !queryPart.equals(queryName)) {	30✔
135	throw new InvalidGrlcSpecException("Query part doesn't match query name: " + queryPart + " / " + queryName);	27✔
136	}
137
138	final Set<String> placeholders = new HashSet<>();	12✔
139	try {
140	ParsedQuery query = new SPARQLParser().parseQuery(queryContent, null);	24✔
141	isConstructQuery = query instanceof ParsedGraphQuery;	12✔
142	query.getTupleExpr().visitChildren(new AbstractSimpleQueryModelVisitor<>() {	42✔
143
144	@Override
145	public void meet(Var node) throws RuntimeException {
146	super.meet(node);	9✔
147	if (!node.isConstant() && !node.isAnonymous() && node.getName().startsWith("_")) {	33!
148	placeholders.add(node.getName());	×
149	}
150	}	3✔
151
152	});
153	} catch (MalformedQueryException ex) {	×
154	throw new InvalidGrlcSpecException("Invalid SPARQL string", ex);	×
155	}	3✔
156	List<String> placeholdersListPre = new ArrayList<>(placeholders);	15✔
157	Collections.sort(placeholdersListPre);	6✔
158	placeholdersListPre.sort(Comparator.comparing(String::length));	12✔
159	placeholdersList = Collections.unmodifiableList(placeholdersListPre);	12✔
160	}	3✔
161
162	/**
163	* Returns the grlc spec as a string.
164	*
165	* @return grlc specification string
166	*/
167	public String getSpec() {
168	String s = "";	6✔
169	if (queryPart.isEmpty()) {	12✔
170	if (label == null) {	9!
171	s += "title: \"untitled query\"\n";	×
172	} else {
173	s += "title: \"" + escapeLiteral(label) + "\"\n";	18✔
174	}
175	s += "description: \"" + escapeLiteral(desc) + "\"\n";	18✔
176	StringBuilder userName = new StringBuilder();	12✔
177	Set<IRI> creators = SimpleCreatorPattern.getCreators(np);	12✔
178	for (IRI userIri : creators) {	30✔
179	userName.append(", ").append(userIri);	18✔
180	}	3✔
181	if (!userName.isEmpty()) {	9!
182	userName = new StringBuilder(userName.substring(2));	21✔
183	}
184	String url = "";	6✔
185	if (!creators.isEmpty()) {	9!
186	url = creators.iterator().next().stringValue();	18✔
187	}
188	s += "contact:\n";	9✔
189	s += " name: \"" + escapeLiteral(userName.toString()) + "\"\n";	18✔
190	s += " url: " + url + "\n";	12✔
191	if (license != null) {	9!
192	s += "licence: " + license + "\n";	15✔
193	}
194	s += "queries:\n";	9✔
195	s += " - " + nanopubQueryUrl + requestUrlBase + artifactCode + "/" + queryName + ".rq";	30✔
196	} else if (queryPart.equals(queryName)) {	21!
197	if (label != null) {	9!
198	s += "#+ summary: \"" + escapeLiteral(label) + "\"\n";	18✔
199	}
200	if (desc != null) {	9!
201	s += "#+ description: \"" + escapeLiteral(desc) + "\"\n";	18✔
202	}
203	if (license != null) {	9!
204	s += "#+ licence: " + license + "\n";	15✔
205	}
206	if (endpoint != null) {	9!
207	s += "#+ endpoint: " + endpoint + "\n";	15✔
208	}
209	s += "\n";	9✔
210	s += queryContent;	18✔
211	} else {
212	throw new RuntimeException("Unexpected queryPart: " + queryPart);	×
213	}
214	return s;	6✔
215	}
216
217	/**
218	* Returns the request parameters.
219	*
220	* @return the request parameters
221	*/
222	public MultiMap getParameters() {
223	return parameters;	9✔
224	}
225
226	/**
227	* Returns the nanopub.
228	*
229	* @return the nanopub
230	*/
231	public Nanopub getNanopub() {
232	return np;	9✔
233	}
234
235	/**
236	* Returns the artifact code.
237	*
238	* @return the artifact code
239	*/
240	public String getArtifactCode() {
241	return artifactCode;	9✔
242	}
243
244	/**
245	* Returns the label.
246	*
247	* @return the label
248	*/
249	public String getLabel() {
250	return label;	9✔
251	}
252
253	/**
254	* Returns the description.
255	*
256	* @return the description
257	*/
258	public String getDescription() {
259	return desc;	9✔
260	}
261
262	/**
263	* Returns the query name.
264	*
265	* @return the query name
266	*/
267	public String getQueryName() {
268	return queryName;	9✔
269	}
270
271	/**
272	* Returns the list of placeholders.
273	*
274	* @return the list of placeholders
275	*/
276	public List<String> getPlaceholdersList() {
277	return placeholdersList;	9✔
278	}
279
280	/**
281	* Returns the repository name derived from the endpoint URL.
282	*
283	* @return the repository name
284	*/
285	public String getRepoName() {
286	return endpoint.replaceAll("/", "_").replaceFirst("^.*_repo_", "");	27✔
287	}
288
289	/**
290	* Returns the query content.
291	*
292	* @return the query content
293	*/
294	public String getQueryContent() {
295	return queryContent;	9✔
296	}
297
298	public boolean isConstructQuery() {
299	return isConstructQuery;	9✔
300	}
301
302	/**
303	* Expands the query by replacing the placeholders with the provided parameter values.
304	*
305	* @return the expanded query
306	* @throws InvalidGrlcSpecException if a non-optional placeholder is missing a value
307	*/
308	public String expandQuery() throws InvalidGrlcSpecException {
309	String expandedQueryContent = queryContent;	×
310	logger.info("Expanding grlc query with parameters: {}", parameters);	×
311	for (String ph : placeholdersList) {	×
312	logger.info("Processing placeholder <{}> associated to parameter with name <{}>", ph, getParamName(ph));	×
313	if (isMultiPlaceholder(ph)) {	×
314	// TODO multi placeholders need proper documentation
315	List<String> val = parameters.getAll(getParamName(ph));	×
316	if (!isOptionalPlaceholder(ph) && val.isEmpty()) {	×
317	throw new InvalidGrlcSpecException("Missing value for non-optional placeholder: " + ph);	×
318	}
319	if (val.isEmpty()) {	×
320	expandedQueryContent = expandedQueryContent.replaceAll("values\\s\\?" + ph + "\\s\\{\\s\\}(\\s\\.)?", "");	×
321	continue;	×
322	}
323	String valueList = "";	×
324	for (String v : val) {	×
325	if (isIriPlaceholder(ph)) {	×
326	valueList += serializeIri(v) + " ";	×
327	} else {
328	valueList += serializeLiteral(v) + " ";	×
329	}
330	}	×
331	expandedQueryContent = expandedQueryContent.replaceAll("values\\s\\?" + ph + "\\s\\{\\s*\\}", "values ?" + ph + " { " + escapeSlashes(valueList) + "}");	×
332	} else {	×
333	String val = parameters.get(getParamName(ph));	×
334	logger.info("Value for placeholder <{}>: {}", ph, val);	×
335	if (!isOptionalPlaceholder(ph) && val == null) {	×
336	throw new InvalidGrlcSpecException("Missing value for non-optional placeholder: " + ph);	×
337	}
338	if (val == null) {	×
339	continue;	×
340	}
341	if (isIriPlaceholder(ph)) {	×
342	expandedQueryContent = expandedQueryContent.replaceAll("\\?" + ph, escapeSlashes(serializeIri(val)));	×
343	} else {
344	expandedQueryContent = expandedQueryContent.replaceAll("\\?" + ph, escapeSlashes(serializeLiteral(val)));	×
345	}
346	}
347	}	×
348	return expandedQueryContent;	×
349	}
350
351	/**
352	* Escapes a literal string for SPARQL.
353	*
354	* @param s The string
355	* @return The escaped string
356	*/
357	public static String escapeLiteral(String s) {
358	return s.replace("\\", "\\\\").replace("\n", "\\n").replace("\"", "\\\"");	33✔
359	}
360
361	/**
362	* Checks whether the given placeholder is an optional placeholder.
363	*
364	* @param placeholder The placeholder name
365	* @return true if it is an optional placeholder, false otherwise
366	*/
367	public static boolean isOptionalPlaceholder(String placeholder) {
368	return placeholder.startsWith("__");	12✔
369	}
370
371	/**
372	* Checks whether the given placeholder is a multi-value placeholder.
373	*
374	* @param placeholder The placeholder name
375	* @return true if it is a multi-value placeholder, false otherwise
376	*/
377	public static boolean isMultiPlaceholder(String placeholder) {
378	return placeholder.endsWith("_multi") \|\| placeholder.endsWith("_multi_iri");	36✔
379	}
380
381	/**
382	* Checks whether the given placeholder is an IRI placeholder.
383	*
384	* @param placeholder The placeholder name
385	* @return true if it is an IRI placeholder, false otherwise
386	*/
387	public static boolean isIriPlaceholder(String placeholder) {
388	return placeholder.endsWith("_iri");	12✔
389	}
390
391	/**
392	* Returns the parameter name for the given placeholder.
393	*
394	* @param placeholder The placeholder name
395	* @return The parameter name
396	*/
397	public static String getParamName(String placeholder) {
398	return placeholder.replaceFirst("^_+", "").replaceFirst("_iri$", "").replaceFirst("_multi$", "");	33✔
399	}
400
401	/**
402	* Serializes an IRI string for SPARQL.
403	*
404	* @param iriString The IRI string
405	* @return The serialized IRI
406	*/
407	public static String serializeIri(String iriString) {
408	return "<" + iriString + ">";	9✔
409	}
410
411	/**
412	* Escapes slashes in a string.
413	*
414	* @param string The string
415	* @return The escaped string
416	*/
417	private static String escapeSlashes(String string) {
418	return string.replace("\\", "\\\\");	×
419	}
420
421	/**
422	* Serializes a literal string for SPARQL.
423	*
424	* @param literalString The literal string
425	* @return The serialized literal
426	*/
427	public static String serializeLiteral(String literalString) {
428	return "\"" + escapeLiteral(literalString) + "\"";	12✔
429	}
430
431	/**
432	* Resolves the latest version of a nanopub by following the supersedes chain in the local store.
433	* Uses a single SPARQL query with a property path to find the latest non-invalidated version
434	* signed by the same key. If no result is found locally, or if the local store is unavailable,
435	* returns the original URI.
436	*
437	* @param nanopubUri the URI of the nanopub to resolve
438	* @return the URI of the latest version
439	*/
440	static String getLatestVersionIdLocally(String nanopubUri) {
441	logger.info("Resolving latest version locally for: {}", nanopubUri);	12✔
442	try {
443	RepositoryConnection conn = TripleStore.get().getRepoConnection("meta");	×
444	try (conn) {	×
445	String query =	×
446	"SELECT ?latest ?date WHERE { " +
447	"GRAPH <" + NPA.GRAPH + "> { " +
448	"<" + nanopubUri + "> <" + NPA.HAS_VALID_SIGNATURE_FOR_PUBLIC_KEY + "> ?pubkey . " +
449	"?latest <" + NPA.HAS_VALID_SIGNATURE_FOR_PUBLIC_KEY + "> ?pubkey . " +
450	"FILTER NOT EXISTS { ?npx <" + NPX.INVALIDATES + "> ?latest ; " +
451	"<" + NPA.HAS_VALID_SIGNATURE_FOR_PUBLIC_KEY + "> ?pubkey . } " +
452	"?latest <" + DCTERMS.CREATED + "> ?date . " +
453	"} " +
454	"GRAPH <" + NPA.NETWORK_GRAPH + "> { " +
455	"?latest (<" + NPX.SUPERSEDES + ">)* <" + nanopubUri + "> . " +
456	"} " +
457	"} ORDER BY DESC(?date) LIMIT 1";
458	TupleQueryResult r = conn.prepareTupleQuery(QueryLanguage.SPARQL, query).evaluate();	×
459	try (r) {	×
460	if (r.hasNext()) {	×
461	String latestUri = r.next().getBinding("latest").getValue().stringValue();	×
462	logger.info("Resolved latest version: {}", latestUri);	×
463	return latestUri;	×
464	}
465	}	×
466	logger.info("No latest version found locally for: {}", nanopubUri);	×
467	return nanopubUri;	×
468	}	×
469	} catch (Exception ex) {	3✔
470	logger.warn("Could not resolve latest version locally, using original version: {}", ex.getMessage());	15✔
471	return nanopubUri;	6✔
472	}
473	}
474
475	}

knowledgepixels / nanopub-query / 23233444105

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