22871832647

Committed 09 Mar 2026 07:50PM UTC coverage: 70.256% (-0.4%) from 70.691%

Build # 22871832647

Build Type

Pull #59

github

Committed by

web-flow

Commit Message

Merge ecc13bbfe into c5531c09a

Pull Request Pull Request #59: Fix api-version=latest hanging for OpenAPI links

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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.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.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.nanopub.Nanopub;
import org.nanopub.SimpleCreatorPattern;
import org.nanopub.extra.server.GetNanopub;
import org.eclipse.rdf4j.query.QueryLanguage;
import org.eclipse.rdf4j.query.TupleQueryResult;
import org.eclipse.rdf4j.repository.RepositoryConnection;
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);
        }

    }

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

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

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

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

knowledgepixels / nanopub-query / 22871832647

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