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knowledgepixels / nanodash / 17424747928

03 Sep 2025 06:13AM UTC coverage: 12.048% (-0.02%) from 12.066%
17424747928

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github

tkuhn
Update dependencies and adapt to new exceptions in nanopub-java

331 of 3866 branches covered (8.56%)

Branch coverage included in aggregate %.

967 of 6908 relevant lines covered (14.0%)

0.61 hits per line

Source File
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77.78
src/main/java/com/knowledgepixels/nanodash/QueryApiAccess.java
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package com.knowledgepixels.nanodash;
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import org.apache.commons.lang3.tuple.Pair;
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import org.eclipse.rdf4j.model.IRI;
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import org.nanopub.extra.services.APINotReachableException;
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import org.nanopub.extra.services.ApiResponse;
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import org.nanopub.extra.services.FailedApiCallException;
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import org.nanopub.extra.services.NotEnoughAPIInstancesException;
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import org.nanopub.extra.services.QueryAccess;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import java.util.HashMap;
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import java.util.Map;
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import java.util.concurrent.ConcurrentHashMap;
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import java.util.concurrent.ConcurrentMap;
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/**
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 * Utility class for accessing and managing API queries.
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 * Provides methods to retrieve query results, manage query IDs, and fetch the latest versions of nanopublications.
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 */
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public class QueryApiAccess {
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    private QueryApiAccess() {
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    }  // no instances allowed
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    private static ConcurrentMap<String, String> queryIds = new ConcurrentHashMap<>();
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    private static final Logger logger = LoggerFactory.getLogger(QueryApiAccess.class);
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    private static ConcurrentMap<String, Pair<Long, String>> latestVersionMap = new ConcurrentHashMap<>();
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    private static final String queryIriPattern = "^(.*[^A-Za-z0-9-_])(RA[A-Za-z0-9-_]{43})[/#]([^/#]+)$";
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    static {
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        // TODO Load this dynamically somehow at some point:
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        load("RAe-oA5eSmkCXCALZ99-0k4imnlI74KPqURfhHOmnzo6A/get-latest-nanopubs-from-pubkeys");
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        load("RAuy4N1h4vZ1wgBUMvTiWw2y_Y0_5oFYRTwdq-xj2qqNM/get-latest-nanopubs-from-userid");
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        load("RAZbyFSenuKSRMLGlRfrbeu6vQ6g2IEECYZ2zSGcIBIhQ/get-accepted-nanopubs-by-author");
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        load("RAiCBvPL2hRGzI8g5L68O-C9yEXryC_vG35GdEm5jtH_s/get-user-stats-from-pubkeys");  // Deactivated for now...
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        load("RA3U23LL3xbNwsu92fAqsKb0kagOud4f9TlRQq3evNJck/get-user-stats-from-userid");  // Deactivated for now...
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        load("RAcNvmEiUNUb2a7O4fwRvy2x2BCN640AC880fTzFworr8/get-top-creators-last30d");
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        load("RAmhy4KQe6I80bA2Da4JziYyKBoXuXIzqo57GDSVgLfDg/get-top-authors");
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        load("RA7oUCHG8TEjVQpGTUN5sfu3_IQmza3aSBSCxfJdBc3Rs/get-most-recent-nanopubs");
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        load("RA52cg2OzJucmpCb7KSKTgfPV5HKIjsFcmww_rxb7v5zU/get-latest-accepted");
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        load("RAPGhXDRzeGu-Qk0AkjleEtxMxqAvJ-dZn7985gzAbyhs/get-publisher-version");
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        load("RAvL7pe2ppsfq4mVWTdJjssYGsjrmliNd_sZO2ytLvg1Y/get-most-used-templates-last30d");
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        load("RANn4Mu8r8bqJA9KJMGXTQAEGAEvtNKGFsuhRIC6BRIOo/get-latest-nanopubs-by-type");
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        load("RAiRsB2YywxjsBMkVRTREJBooXhf2ZOHoUs5lxciEl37I/get-latest-version-of-np");
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        load("RA0aZxyh_I0rCJyBepXOWC2tGdI5YYHORFCC-qBR8xHZA/get-all-user-intros");
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        load("RA-tlMmQA7iT2wR2aS3PlONrepX7vdXbkzeWluea7AECg/get-suggested-templates-to-get-started");
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        load("RAtIndAeo8zYnEvTjFRaHD2AlenvkJHlw6P52JWR_l5dQ/get-type-overview-last-12-months");
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        load("RAn3agwsH2yk-8132RJApGYxdPSHHCXDAIYiCaSBBo6tg/get-approved-nanopubs");
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        load("RAz1ogtMxSTKSOYwHAfD5M3Y-vd1vd46OZta_vvbqh8kY/find-uri-references");
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        load("RAE35dYJQlpnqim7VeKuu07E9I1LQUZpkdYQR4RvU3KMU/get-nanopubs-by-type");
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        load("RALZXWg5lZoJoQ0VHL5mpDgNxYpqU6FoDLWGp4rs8A6b8/get-introducing-nanopub");
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        load("RAWruhiSmyzgZhVRs8QY8YQPAgHzTfl7anxII1de-yaCs/fulltext-search-on-labels");
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        load("RAVEmFh3d6qonTFQ5S9SVqXZh0prrH1YLhSSs0dJvyvpM/find-things");
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        load("RAjt1H9rCSr6A9VGzlhye00zPdH69JdGc3kd_2VjDmzVg/get-instances");
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        load("RAH06iUwnvj_pRARY15ayJAY5tuJau3rCvHhPPhe49fVI/get-classes-for-thing");
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        load("RAJStXEm1wZcg34ZLPqe00VPSzIVCwC2rrxdj_JR8v5DY/find-referencing-nanopubs");  // not yet used...
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        load("RAtftxAXJubB4rlm9fOvvHNVIkXvWQLC6Ag_MiV7HL0ow/get-labels-for-thing");  // not yet used...
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        load("RARtWHRzNY5hh31X2VB5eOCJAdp9Cjv4CakA0Idqz69MI/get-templates-with-uri");
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        load("RAWH0fe1RCpoOgaJE1B2qfTzzdTiBUUK7iIk6l7Zll9mg/get-newer-versions-of-np");
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        load("RAQqjXQYlxYQeI4Y3UQy9OrD5Jx1E3PJ8KwKKQlWbiYSw/get-queries");
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        load("RAzXDzCHoZmJITgYYquLwDDkSyNf3eKKQz9NfQPYB1cyE/get-latest-thing-nanopub");
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        load("RAnpimW7SPwaum2fefdS6_jpzYxcTRGjE-pmgNTL_BBJU/get-projects");
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        load("RAJmZoM0xCGE8OL6EgmQBOd1M58ggNkwZ0IUqHOAPRfvE/get-parts");
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        load("RA6bgrU3Ezfg5VAiLru0BFYHaSj6vZU6jJTscxNl8Wqvc/get-assertion-templates");
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        load("RA4bt3MQRnEPC2nSsdbCJc74wT-e1w68dSCpYVyvG0274/get-provenance-templates");
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        load("RAMcdiJpvvk8424AJIH1jsDUQVcPYOLRw0DNnZt_ND_LQ/get-pubinfo-templates");
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        load("RAwfurJs7mlYWdW4fSpd6hM1AGjQ_2QMiy3VyOP6vdrlE/get-owners-of-project");
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        load("RAHooeYnQyfu4gXNg5g32PlQRlqsfEblsCNG2DjSYF-y0/get-members-of-project");
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    }
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    /**
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     * Loads a query ID into the queryIds map.
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     *
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     * @param queryId The query ID to load.
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     */
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    static void load(String queryId) {
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        queryIds.put(queryId.substring(46), queryId);
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    }
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    /**
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     * Forces the retrieval of an API response for a given query name and parameters.
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     * Retries until a valid response is received.
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     *
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     * @param queryName The name of the query.
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     * @return The API response.
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     */
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    public static ApiResponse forcedGet(String queryName) {
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        return forcedGet(queryName, new HashMap<>());
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    }
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    /**
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     * Forces the retrieval of an API response for a given query name and a single parameter.
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     * Retries until a valid response is received.
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     *
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     * @param queryName  The name of the query.
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     * @param paramKey   The key of the parameter.
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     * @param paramValue The value of the parameter.
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     * @return The API response.
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     */
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    public static ApiResponse forcedGet(String queryName, String paramKey, String paramValue) {
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        Map<String, String> params = new HashMap<>();
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        params.put(paramKey, paramValue);
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        return forcedGet(queryName, params);
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    }
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    /**
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     * Forces the retrieval of an API response for a given query name and parameters.
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     * Retries until a valid response is received.
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     *
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     * @param queryName The name of the query.
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     * @param params    The parameters for the query.
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     * @return The API response.
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     */
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    public static ApiResponse forcedGet(String queryName, Map<String, String> params) {
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        while (true) {
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            ApiResponse resp = null;
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            try {
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                resp = QueryApiAccess.get(queryName, params);
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            } catch (Exception ex) {
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                // TODO We should be more specific about which exceptions we catch here
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                //      and generally improve this, as this could hang forever.
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                logger.error("Error while forcing API get for query '{}' with params {}", queryName, params, ex);
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            }
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            if (resp != null) return resp;
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            try {
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                Thread.sleep(100);
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            } catch (InterruptedException ex) {
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                logger.error("Interrupted while forcing API get for query '{}' with params {}", queryName, params, ex);
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            }
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        }
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    }
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    /**
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     * Retrieves an API response for a given query name.
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     *
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     * @param queryName The name of the query.
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     * @return The API response.
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     * @throws org.nanopub.extra.services.FailedApiCallException If the API call fails.
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     */
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    public static ApiResponse get(String queryName) throws FailedApiCallException, APINotReachableException, NotEnoughAPIInstancesException {
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        return get(queryName, new HashMap<>());
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    }
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    /**
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     * Retrieves an API response for a given query name and a single parameter.
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     *
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     * @param queryName  The name of the query.
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     * @param paramKey   The key of the parameter.
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     * @param paramValue The value of the parameter.
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     * @return The API response.
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     * @throws org.nanopub.extra.services.FailedApiCallException If the API call fails.
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     */
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    public static ApiResponse get(String queryName, String paramKey, String paramValue) throws FailedApiCallException, APINotReachableException, NotEnoughAPIInstancesException {
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        Map<String, String> params = new HashMap<>();
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        params.put(paramKey, paramValue);
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        return get(queryName, params);
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    }
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    /**
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     * Retrieves an API response for a given query name and parameters.
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     *
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     * @param queryName The name of the query.
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     * @param params    The parameters for the query.
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     * @return The API response.
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     * @throws org.nanopub.extra.services.FailedApiCallException If the API call fails.
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     */
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    public static ApiResponse get(String queryName, Map<String, String> params) throws FailedApiCallException, APINotReachableException, NotEnoughAPIInstancesException {
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        String queryId;
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        if (queryName.matches("^RA[A-Za-z0-9-_]{43}/.*$")) {
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            queryId = queryName;
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        } else if (queryIds.containsKey(queryName)) {
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            queryId = queryIds.get(queryName);
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        } else {
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            throw new IllegalArgumentException("Query name not known: " + queryName);
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        }
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        return QueryAccess.get(queryId, params);
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    }
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    /**
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     * Retrieves the latest version ID of a given nanopublication.
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     *
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     * @param nanopubId The ID of the nanopublication.
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     * @return The latest version ID.
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     */
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    public static String getLatestVersionId(String nanopubId) {
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        long currentTime = System.currentTimeMillis();
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        if (!latestVersionMap.containsKey(nanopubId) || currentTime - latestVersionMap.get(nanopubId).getLeft() > 1000 * 60) {
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            // Re-fetch if existing value is older than 1 minute
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            Map<String, String> params = new HashMap<>();
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            params.put("np", nanopubId);
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            try {
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                ApiResponse r = get("get-latest-version-of-np", params);
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                if (r.getData().size() != 1) return nanopubId;
5!
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                String l = r.getData().get(0).get("latest");
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                latestVersionMap.put(nanopubId, Pair.of(currentTime, l));
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            } catch (Exception ex) {
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                logger.error("Error while getting latest version of nanopub '{}'", nanopubId, ex);
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                return nanopubId;
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            }
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        }
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        return latestVersionMap.get(nanopubId).getRight();
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    }
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    /**
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     * Extracts the query ID from a given query IRI.
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     *
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     * @param queryIri The query IRI.
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     * @return The query ID, or null if the IRI is invalid.
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     */
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    public static String getQueryId(IRI queryIri) {
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        if (queryIri == null) return null;
×
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        if (!queryIri.stringValue().matches(queryIriPattern)) return null;
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        return queryIri.stringValue().replaceFirst(queryIriPattern, "$2/$3");
×
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    }
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    /**
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     * Retrieves the query ID for a given query name.
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     *
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     * @param queryName The name of the query.
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     * @return The query ID, or null if the query name is unknown.
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     */
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    public static String getQueryId(String queryName) {
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        return queryIds.get(queryName);
5✔
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    }
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    /**
231
     * Extracts the query name from a given query IRI.
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     *
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     * @param queryIri The query IRI.
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     * @return The query name, or null if the IRI is invalid.
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     */
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    public static String getQueryName(IRI queryIri) {
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        if (queryIri == null) return null;
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        if (!queryIri.stringValue().matches(queryIriPattern)) return null;
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        return queryIri.stringValue().replaceFirst(queryIriPattern, "$3");
6✔
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    }
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}
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