23632443330

Committed 27 Mar 2026 05:20AM UTC coverage: 66.744% (-0.3%) from 67.082%

Build # 23632443330

Build Type

Pull #61

github

Committed by

web-flow

Commit Message

Merge 59686a478 into 1927e9847

Pull Request Pull Request #61: feat: preview unpublished nanopub queries via URL parameter

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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.rio.RDFFormat;
import org.nanopub.MalformedNanopubException;
import org.eclipse.rdf4j.repository.RepositoryConnection;
import org.nanopub.Nanopub;
import org.nanopub.NanopubImpl;
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.io.ByteArrayInputStream;
import java.io.IOException;
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}/)(.*)?$", "$3");
        queryPart = queryPart.replaceFirst(".rq$", "");

        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 = GetNanopub.get(artifactCode);
        }
        // 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 = 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.rio.RDFFormat;
21	import org.nanopub.MalformedNanopubException;
22	import org.eclipse.rdf4j.repository.RepositoryConnection;
23	import org.nanopub.Nanopub;
24	import org.nanopub.NanopubImpl;
25	import org.nanopub.SimpleCreatorPattern;
26	import org.nanopub.extra.server.GetNanopub;
27	import org.nanopub.vocabulary.NPA;
28	import org.nanopub.vocabulary.NPX;
29	import org.slf4j.Logger;
30	import org.slf4j.LoggerFactory;
31
32	import java.io.ByteArrayInputStream;
33	import java.io.IOException;
34	import java.util.*;
35
36	//TODO merge this class with GrlcQuery of Nanodash and move to a library like nanopub-java
37
38	/**
39	* This class produces a page with the grlc specification. This is needed internally to tell grlc
40	* how to execute a particular query template.
41	*/
42	public class GrlcSpec {
43
44	private static final ValueFactory vf = SimpleValueFactory.getInstance();	6✔
45
46	private static final Logger logger = LoggerFactory.getLogger(GrlcSpec.class);	9✔
47
48	/**
49	* Exception for invalid grlc specifications.
50	*/
51	public static class InvalidGrlcSpecException extends Exception {
52
53	private InvalidGrlcSpecException(String msg) {
54	super(msg);	9✔
55	}	3✔
56
57	private InvalidGrlcSpecException(String msg, Throwable throwable) {
58	super(msg, throwable);	×
59	}	×
60
61	}
62
63	/**
64	* URL for the given Nanopub Query instance, needed for internal coordination.
65	*/
66	public static final String nanopubQueryUrl = Utils.getEnvString("NANOPUB_QUERY_URL", "http://query:9393/");	15✔
67
68	private static final String NANOPUB_QUERY_REPO_URL = "https://w3id.org/np/l/nanopub-query-1.1/repo/";
69
70	private MultiMap parameters;
71	private Nanopub np;
72	private String requestUrlBase;
73	private String artifactCode;
74	private String queryPart;
75	private String queryName;
76	private String label;
77	private String desc;
78	private String license;
79	private String queryContent;
80	private String endpoint;
81	private List<String> placeholdersList;
82	private boolean isConstructQuery;
83
84	/**
85	* Creates a new page instance.
86	*
87	* @param requestUrl The request URL
88	* @param parameters The URL request parameters
89	*/
90	public GrlcSpec(String requestUrl, MultiMap parameters) throws InvalidGrlcSpecException {	6✔
91	this.parameters = parameters;	9✔
92	requestUrl = requestUrl.replaceFirst("\\?.*$", "");	15✔
93	if (!requestUrl.matches("./RA[A-Za-z0-9\\-_]{43}/(.)?")) {	12✔
94	throw new InvalidGrlcSpecException("Invalid grlc API request: " + requestUrl);	18✔
95	}
96	artifactCode = requestUrl.replaceFirst("^(./)(RA[A-Za-z0-9\\-_]{43})/(.)?$", "$2");	18✔
97	requestUrlBase = requestUrl.replaceFirst("^/(./)(RA[A-Za-z0-9\\-_]{43})/(.)?$", "$1");	18✔
98
99	queryPart = requestUrl.replaceFirst("^(./)(RA[A-Za-z0-9\\-_]{43}/)(.)?$", "$3");	18✔
100	queryPart = queryPart.replaceFirst(".rq$", "");	21✔
101
102	String nanopubParam = parameters.get("_nanopub_trig");	12✔
103	if (nanopubParam != null && !nanopubParam.isEmpty()) {	6!
104	try {
105	byte[] trig = Base64.getUrlDecoder().decode(nanopubParam);	×
106	np = new NanopubImpl(new ByteArrayInputStream(trig), RDFFormat.TRIG);	×
107	} catch (MalformedNanopubException \| IOException \| IllegalArgumentException ex) {	×
108	throw new InvalidGrlcSpecException("Failed to parse nanopub from 'nanopub' parameter", ex);	×
109	}	×
110	} else {
111	np = GetNanopub.get(artifactCode);	15✔
112	}
113	// TODO rename "api-version" to "_api_version" for consistency
114	if (parameters.get("api-version") != null && parameters.get("api-version").equals("latest")) {	30✔
115	String latestUri = getLatestVersionIdLocally(np.getUri().stringValue());	18✔
116	if (!latestUri.equals(np.getUri().stringValue())) {	21!
117	np = GetNanopub.get(TrustyUriUtils.getArtifactCode(latestUri));	×
118	}
119	artifactCode = TrustyUriUtils.getArtifactCode(np.getUri().stringValue());	21✔
120	}
121	for (Statement st : np.getAssertion()) {	36✔
122	if (!st.getSubject().stringValue().startsWith(np.getUri().stringValue())) {	27!
123	continue;	×
124	}
125	String qn = st.getSubject().stringValue().replaceFirst("^.[#/](.)$", "$1");	21✔
126	if (queryName != null && !qn.equals(queryName)) {	24!
127	throw new InvalidGrlcSpecException("Subject suffixes don't match: " + queryName);	×
128	}
129	queryName = qn;	9✔
130	if (st.getPredicate().equals(RDFS.LABEL)) {	15✔
131	label = st.getObject().stringValue();	18✔
132	} else if (st.getPredicate().equals(DCTERMS.DESCRIPTION)) {	15✔
133	desc = st.getObject().stringValue();	18✔
134	} else if (st.getPredicate().equals(DCTERMS.LICENSE) && st.getObject() instanceof IRI) {	27!
135	license = st.getObject().stringValue();	18✔
136	} else if (st.getPredicate().equals(KPXL_GRLC.SPARQL)) {	15✔
137	// TODO Improve this:
138	queryContent = st.getObject().stringValue().replace(NANOPUB_QUERY_REPO_URL, nanopubQueryUrl + "repo/");	30✔
139	} else if (st.getPredicate().equals(KPXL_GRLC.ENDPOINT) && st.getObject() instanceof IRI) {	27!
140	endpoint = st.getObject().stringValue();	15✔
141	if (endpoint.startsWith(NANOPUB_QUERY_REPO_URL)) {	15!
142	endpoint = endpoint.replace(NANOPUB_QUERY_REPO_URL, nanopubQueryUrl + "repo/");	27✔
143	} else {
144	throw new InvalidGrlcSpecException("Invalid/non-recognized endpoint: " + endpoint);	×
145	}
146	}
147	}	3✔
148
149	if (!queryPart.isEmpty() && !queryPart.equals(queryName)) {	30✔
150	throw new InvalidGrlcSpecException("Query part doesn't match query name: " + queryPart + " / " + queryName);	27✔
151	}
152
153	final Set<String> placeholders = new HashSet<>();	12✔
154	try {
155	ParsedQuery query = new SPARQLParser().parseQuery(queryContent, null);	24✔
156	isConstructQuery = query instanceof ParsedGraphQuery;	12✔
157	query.getTupleExpr().visitChildren(new AbstractSimpleQueryModelVisitor<>() {	42✔
158
159	@Override
160	public void meet(Var node) throws RuntimeException {
161	super.meet(node);	9✔
162	if (!node.isConstant() && !node.isAnonymous() && node.getName().startsWith("_")) {	33!
163	placeholders.add(node.getName());	×
164	}
165	}	3✔
166
167	});
168	} catch (MalformedQueryException ex) {	×
169	throw new InvalidGrlcSpecException("Invalid SPARQL string", ex);	×
170	}	3✔
171	List<String> placeholdersListPre = new ArrayList<>(placeholders);	15✔
172	Collections.sort(placeholdersListPre);	6✔
173	placeholdersListPre.sort(Comparator.comparing(String::length));	12✔
174	placeholdersList = Collections.unmodifiableList(placeholdersListPre);	12✔
175	}	3✔
176
177	/**
178	* Returns the grlc spec as a string.
179	*
180	* @return grlc specification string
181	*/
182	public String getSpec() {
183	String s = "";	6✔
184	if (queryPart.isEmpty()) {	12✔
185	if (label == null) {	9!
186	s += "title: \"untitled query\"\n";	×
187	} else {
188	s += "title: \"" + escapeLiteral(label) + "\"\n";	18✔
189	}
190	s += "description: \"" + escapeLiteral(desc) + "\"\n";	18✔
191	StringBuilder userName = new StringBuilder();	12✔
192	Set<IRI> creators = SimpleCreatorPattern.getCreators(np);	12✔
193	for (IRI userIri : creators) {	30✔
194	userName.append(", ").append(userIri);	18✔
195	}	3✔
196	if (!userName.isEmpty()) {	9!
197	userName = new StringBuilder(userName.substring(2));	21✔
198	}
199	String url = "";	6✔
200	if (!creators.isEmpty()) {	9!
201	url = creators.iterator().next().stringValue();	18✔
202	}
203	s += "contact:\n";	9✔
204	s += " name: \"" + escapeLiteral(userName.toString()) + "\"\n";	18✔
205	s += " url: " + url + "\n";	12✔
206	if (license != null) {	9!
207	s += "licence: " + license + "\n";	15✔
208	}
209	s += "queries:\n";	9✔
210	s += " - " + nanopubQueryUrl + requestUrlBase + artifactCode + "/" + queryName + ".rq";	30✔
211	} else if (queryPart.equals(queryName)) {	21!
212	if (label != null) {	9!
213	s += "#+ summary: \"" + escapeLiteral(label) + "\"\n";	18✔
214	}
215	if (desc != null) {	9!
216	s += "#+ description: \"" + escapeLiteral(desc) + "\"\n";	18✔
217	}
218	if (license != null) {	9!
219	s += "#+ licence: " + license + "\n";	15✔
220	}
221	if (endpoint != null) {	9!
222	s += "#+ endpoint: " + endpoint + "\n";	15✔
223	}
224	s += "\n";	9✔
225	s += queryContent;	18✔
226	} else {
227	throw new RuntimeException("Unexpected queryPart: " + queryPart);	×
228	}
229	return s;	6✔
230	}
231
232	/**
233	* Returns the request parameters.
234	*
235	* @return the request parameters
236	*/
237	public MultiMap getParameters() {
238	return parameters;	9✔
239	}
240
241	/**
242	* Returns the nanopub.
243	*
244	* @return the nanopub
245	*/
246	public Nanopub getNanopub() {
247	return np;	9✔
248	}
249
250	/**
251	* Returns the artifact code.
252	*
253	* @return the artifact code
254	*/
255	public String getArtifactCode() {
256	return artifactCode;	9✔
257	}
258
259	/**
260	* Returns the label.
261	*
262	* @return the label
263	*/
264	public String getLabel() {
265	return label;	9✔
266	}
267
268	/**
269	* Returns the description.
270	*
271	* @return the description
272	*/
273	public String getDescription() {
274	return desc;	9✔
275	}
276
277	/**
278	* Returns the query name.
279	*
280	* @return the query name
281	*/
282	public String getQueryName() {
283	return queryName;	9✔
284	}
285
286	/**
287	* Returns the list of placeholders.
288	*
289	* @return the list of placeholders
290	*/
291	public List<String> getPlaceholdersList() {
292	return placeholdersList;	9✔
293	}
294
295	/**
296	* Returns the repository name derived from the endpoint URL.
297	*
298	* @return the repository name
299	*/
300	public String getRepoName() {
301	return endpoint.replaceAll("/", "_").replaceFirst("^.*_repo_", "");	27✔
302	}
303
304	/**
305	* Returns the query content.
306	*
307	* @return the query content
308	*/
309	public String getQueryContent() {
310	return queryContent;	9✔
311	}
312
313	public boolean isConstructQuery() {
314	return isConstructQuery;	9✔
315	}
316
317	/**
318	* Expands the query by replacing the placeholders with the provided parameter values.
319	*
320	* @return the expanded query
321	* @throws InvalidGrlcSpecException if a non-optional placeholder is missing a value
322	*/
323	public String expandQuery() throws InvalidGrlcSpecException {
324	String expandedQueryContent = queryContent;	×
325	logger.info("Expanding grlc query with parameters: {}", parameters);	×
326	for (String ph : placeholdersList) {	×
327	logger.info("Processing placeholder <{}> associated to parameter with name <{}>", ph, getParamName(ph));	×
328	if (isMultiPlaceholder(ph)) {	×
329	// TODO multi placeholders need proper documentation
330	List<String> val = parameters.getAll(getParamName(ph));	×
331	if (!isOptionalPlaceholder(ph) && val.isEmpty()) {	×
332	throw new InvalidGrlcSpecException("Missing value for non-optional placeholder: " + ph);	×
333	}
334	if (val.isEmpty()) {	×
335	expandedQueryContent = expandedQueryContent.replaceAll("values\\s\\?" + ph + "\\s\\{\\s\\}(\\s\\.)?", "");	×
336	continue;	×
337	}
338	String valueList = "";	×
339	for (String v : val) {	×
340	if (isIriPlaceholder(ph)) {	×
341	valueList += serializeIri(v) + " ";	×
342	} else {
343	valueList += serializeLiteral(v) + " ";	×
344	}
345	}	×
346	expandedQueryContent = expandedQueryContent.replaceAll("values\\s\\?" + ph + "\\s\\{\\s*\\}", "values ?" + ph + " { " + escapeSlashes(valueList) + "}");	×
347	} else {	×
348	String val = parameters.get(getParamName(ph));	×
349	logger.info("Value for placeholder <{}>: {}", ph, val);	×
350	if (!isOptionalPlaceholder(ph) && val == null) {	×
351	throw new InvalidGrlcSpecException("Missing value for non-optional placeholder: " + ph);	×
352	}
353	if (val == null) {	×
354	continue;	×
355	}
356	if (isIriPlaceholder(ph)) {	×
357	expandedQueryContent = expandedQueryContent.replaceAll("\\?" + ph, escapeSlashes(serializeIri(val)));	×
358	} else {
359	expandedQueryContent = expandedQueryContent.replaceAll("\\?" + ph, escapeSlashes(serializeLiteral(val)));	×
360	}
361	}
362	}	×
363	return expandedQueryContent;	×
364	}
365
366	/**
367	* Escapes a literal string for SPARQL.
368	*
369	* @param s The string
370	* @return The escaped string
371	*/
372	public static String escapeLiteral(String s) {
373	return s.replace("\\", "\\\\").replace("\n", "\\n").replace("\"", "\\\"");	33✔
374	}
375
376	/**
377	* Checks whether the given placeholder is an optional placeholder.
378	*
379	* @param placeholder The placeholder name
380	* @return true if it is an optional placeholder, false otherwise
381	*/
382	public static boolean isOptionalPlaceholder(String placeholder) {
383	return placeholder.startsWith("__");	12✔
384	}
385
386	/**
387	* Checks whether the given placeholder is a multi-value placeholder.
388	*
389	* @param placeholder The placeholder name
390	* @return true if it is a multi-value placeholder, false otherwise
391	*/
392	public static boolean isMultiPlaceholder(String placeholder) {
393	return placeholder.endsWith("_multi") \|\| placeholder.endsWith("_multi_iri");	36✔
394	}
395
396	/**
397	* Checks whether the given placeholder is an IRI placeholder.
398	*
399	* @param placeholder The placeholder name
400	* @return true if it is an IRI placeholder, false otherwise
401	*/
402	public static boolean isIriPlaceholder(String placeholder) {
403	return placeholder.endsWith("_iri");	12✔
404	}
405
406	/**
407	* Returns the parameter name for the given placeholder.
408	*
409	* @param placeholder The placeholder name
410	* @return The parameter name
411	*/
412	public static String getParamName(String placeholder) {
413	return placeholder.replaceFirst("^_+", "").replaceFirst("_iri$", "").replaceFirst("_multi$", "");	33✔
414	}
415
416	/**
417	* Serializes an IRI string for SPARQL.
418	*
419	* @param iriString The IRI string
420	* @return The serialized IRI
421	*/
422	public static String serializeIri(String iriString) {
423	return "<" + iriString + ">";	9✔
424	}
425
426	/**
427	* Escapes slashes in a string.
428	*
429	* @param string The string
430	* @return The escaped string
431	*/
432	private static String escapeSlashes(String string) {
433	return string.replace("\\", "\\\\");	×
434	}
435
436	/**
437	* Serializes a literal string for SPARQL.
438	*
439	* @param literalString The literal string
440	* @return The serialized literal
441	*/
442	public static String serializeLiteral(String literalString) {
443	return "\"" + escapeLiteral(literalString) + "\"";	12✔
444	}
445
446	/**
447	* Resolves the latest version of a nanopub by following the supersedes chain in the local store.
448	* Uses a single SPARQL query with a property path to find the latest non-invalidated version
449	* signed by the same key. If no result is found locally, or if the local store is unavailable,
450	* returns the original URI.
451	*
452	* @param nanopubUri the URI of the nanopub to resolve
453	* @return the URI of the latest version
454	*/
455	static String getLatestVersionIdLocally(String nanopubUri) {
456	logger.info("Resolving latest version locally for: {}", nanopubUri);	12✔
457	try {
458	RepositoryConnection conn = TripleStore.get().getRepoConnection("meta");	×
459	try (conn) {	×
460	String query =	×
461	"SELECT ?latest ?date WHERE { " +
462	"GRAPH <" + NPA.GRAPH + "> { " +
463	"<" + nanopubUri + "> <" + NPA.HAS_VALID_SIGNATURE_FOR_PUBLIC_KEY + "> ?pubkey . " +
464	"?latest <" + NPA.HAS_VALID_SIGNATURE_FOR_PUBLIC_KEY + "> ?pubkey . " +
465	"FILTER NOT EXISTS { ?npx <" + NPX.INVALIDATES + "> ?latest ; " +
466	"<" + NPA.HAS_VALID_SIGNATURE_FOR_PUBLIC_KEY + "> ?pubkey . } " +
467	"?latest <" + DCTERMS.CREATED + "> ?date . " +
468	"} " +
469	"GRAPH <" + NPA.NETWORK_GRAPH + "> { " +
470	"?latest (<" + NPX.SUPERSEDES + ">)* <" + nanopubUri + "> . " +
471	"} " +
472	"} ORDER BY DESC(?date) LIMIT 1";
473	TupleQueryResult r = conn.prepareTupleQuery(QueryLanguage.SPARQL, query).evaluate();	×
474	try (r) {	×
475	if (r.hasNext()) {	×
476	String latestUri = r.next().getBinding("latest").getValue().stringValue();	×
477	logger.info("Resolved latest version: {}", latestUri);	×
478	return latestUri;	×
479	}
480	}	×
481	logger.info("No latest version found locally for: {}", nanopubUri);	×
482	return nanopubUri;	×
483	}	×
484	} catch (Exception ex) {	3✔
485	logger.warn("Could not resolve latest version locally, using original version: {}", ex.getMessage());	15✔
486	return nanopubUri;	6✔
487	}
488	}
489
490	}

knowledgepixels / nanopub-query / 23632443330

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