17380144000

Committed 01 Sep 2025 02:12PM UTC coverage: 12.03% (+0.05%) from 11.978%

Build # 17380144000

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push

github

Committed by

ashleycaselli

Commit Message

refactor: replace printStackTrace with logger.error for better error handling

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81.55

src/main/java/com/knowledgepixels/nanodash/QueryApiAccess.java

package com.knowledgepixels.nanodash;

import org.apache.commons.lang3.tuple.Pair;
import org.eclipse.rdf4j.model.IRI;
import org.nanopub.extra.services.ApiResponse;
import org.nanopub.extra.services.FailedApiCallException;
import org.nanopub.extra.services.QueryAccess;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import java.util.HashMap;
import java.util.Map;
import java.util.concurrent.ConcurrentHashMap;
import java.util.concurrent.ConcurrentMap;

/**
 * Utility class for accessing and managing API queries.
 * Provides methods to retrieve query results, manage query IDs, and fetch the latest versions of nanopublications.
 */
public class QueryApiAccess {

    private QueryApiAccess() {
    }  // no instances allowed

    private static ConcurrentMap<String, String> queryIds = new ConcurrentHashMap<>();
    private static final Logger logger = LoggerFactory.getLogger(QueryApiAccess.class);

    private static ConcurrentMap<String, Pair<Long, String>> latestVersionMap = new ConcurrentHashMap<>();

    private static final String queryIriPattern = "^(.*[^A-Za-z0-9-_])(RA[A-Za-z0-9-_]{43})[/#]([^/#]+)$";

    static {
        // TODO Load this dynamically somehow at some point:
        load("RAe-oA5eSmkCXCALZ99-0k4imnlI74KPqURfhHOmnzo6A/get-latest-nanopubs-from-pubkeys");
        load("RAuy4N1h4vZ1wgBUMvTiWw2y_Y0_5oFYRTwdq-xj2qqNM/get-latest-nanopubs-from-userid");
        load("RAZbyFSenuKSRMLGlRfrbeu6vQ6g2IEECYZ2zSGcIBIhQ/get-accepted-nanopubs-by-author");
        load("RAiCBvPL2hRGzI8g5L68O-C9yEXryC_vG35GdEm5jtH_s/get-user-stats-from-pubkeys");  // Deactivated for now...
        load("RA3U23LL3xbNwsu92fAqsKb0kagOud4f9TlRQq3evNJck/get-user-stats-from-userid");  // Deactivated for now...
        load("RAcNvmEiUNUb2a7O4fwRvy2x2BCN640AC880fTzFworr8/get-top-creators-last30d");
        load("RAmhy4KQe6I80bA2Da4JziYyKBoXuXIzqo57GDSVgLfDg/get-top-authors");
        load("RA7oUCHG8TEjVQpGTUN5sfu3_IQmza3aSBSCxfJdBc3Rs/get-most-recent-nanopubs");
        load("RA52cg2OzJucmpCb7KSKTgfPV5HKIjsFcmww_rxb7v5zU/get-latest-accepted");
        load("RAPGhXDRzeGu-Qk0AkjleEtxMxqAvJ-dZn7985gzAbyhs/get-publisher-version");
        load("RAvL7pe2ppsfq4mVWTdJjssYGsjrmliNd_sZO2ytLvg1Y/get-most-used-templates-last30d");
        load("RANn4Mu8r8bqJA9KJMGXTQAEGAEvtNKGFsuhRIC6BRIOo/get-latest-nanopubs-by-type");
        load("RAiRsB2YywxjsBMkVRTREJBooXhf2ZOHoUs5lxciEl37I/get-latest-version-of-np");
        load("RA0aZxyh_I0rCJyBepXOWC2tGdI5YYHORFCC-qBR8xHZA/get-all-user-intros");
        load("RA-tlMmQA7iT2wR2aS3PlONrepX7vdXbkzeWluea7AECg/get-suggested-templates-to-get-started");
        load("RAtIndAeo8zYnEvTjFRaHD2AlenvkJHlw6P52JWR_l5dQ/get-type-overview-last-12-months");
        load("RAn3agwsH2yk-8132RJApGYxdPSHHCXDAIYiCaSBBo6tg/get-approved-nanopubs");
        load("RAz1ogtMxSTKSOYwHAfD5M3Y-vd1vd46OZta_vvbqh8kY/find-uri-references");
        load("RAE35dYJQlpnqim7VeKuu07E9I1LQUZpkdYQR4RvU3KMU/get-nanopubs-by-type");
        load("RALZXWg5lZoJoQ0VHL5mpDgNxYpqU6FoDLWGp4rs8A6b8/get-introducing-nanopub");
        load("RAWruhiSmyzgZhVRs8QY8YQPAgHzTfl7anxII1de-yaCs/fulltext-search-on-labels");
        load("RAVEmFh3d6qonTFQ5S9SVqXZh0prrH1YLhSSs0dJvyvpM/find-things");
        load("RAjt1H9rCSr6A9VGzlhye00zPdH69JdGc3kd_2VjDmzVg/get-instances");
        load("RAH06iUwnvj_pRARY15ayJAY5tuJau3rCvHhPPhe49fVI/get-classes-for-thing");
        load("RAJStXEm1wZcg34ZLPqe00VPSzIVCwC2rrxdj_JR8v5DY/find-referencing-nanopubs");  // not yet used...
        load("RAtftxAXJubB4rlm9fOvvHNVIkXvWQLC6Ag_MiV7HL0ow/get-labels-for-thing");  // not yet used...
        load("RARtWHRzNY5hh31X2VB5eOCJAdp9Cjv4CakA0Idqz69MI/get-templates-with-uri");
        load("RAWH0fe1RCpoOgaJE1B2qfTzzdTiBUUK7iIk6l7Zll9mg/get-newer-versions-of-np");
        load("RAQqjXQYlxYQeI4Y3UQy9OrD5Jx1E3PJ8KwKKQlWbiYSw/get-queries");
        load("RAzXDzCHoZmJITgYYquLwDDkSyNf3eKKQz9NfQPYB1cyE/get-latest-thing-nanopub");
        load("RAnpimW7SPwaum2fefdS6_jpzYxcTRGjE-pmgNTL_BBJU/get-projects");
        load("RAJmZoM0xCGE8OL6EgmQBOd1M58ggNkwZ0IUqHOAPRfvE/get-parts");
        load("RA6bgrU3Ezfg5VAiLru0BFYHaSj6vZU6jJTscxNl8Wqvc/get-assertion-templates");
        load("RA4bt3MQRnEPC2nSsdbCJc74wT-e1w68dSCpYVyvG0274/get-provenance-templates");
        load("RAMcdiJpvvk8424AJIH1jsDUQVcPYOLRw0DNnZt_ND_LQ/get-pubinfo-templates");
    }

    /**
     * Loads a query ID into the queryIds map.
     *
     * @param queryId The query ID to load.
     */
    static void load(String queryId) {
        queryIds.put(queryId.substring(46), queryId);
    }

    /**
     * Forces the retrieval of an API response for a given query name and parameters.
     * Retries until a valid response is received.
     *
     * @param queryName The name of the query.
     * @return The API response.
     */
    public static ApiResponse forcedGet(String queryName) {
        return forcedGet(queryName, new HashMap<>());
    }

    /**
     * Forces the retrieval of an API response for a given query name and parameters.
     * Retries until a valid response is received.
     *
     * @param queryName The name of the query.
     * @param params    The parameters for the query.
     * @return The API response.
     */
    public static ApiResponse forcedGet(String queryName, Map<String, String> params) {
        while (true) {
            ApiResponse resp = null;
            try {
                resp = QueryApiAccess.get(queryName, params);
            } catch (Exception ex) {
                // TODO We should be more specific about which exceptions we catch here
                //      and generally improve this, as this could hang forever.
                logger.error("Error while forcing API get for query '{}' with params {}", queryName, params, ex);
            }
            if (resp != null) return resp;
            try {
                Thread.sleep(100);
            } catch (InterruptedException ex) {
                logger.error("Interrupted while forcing API get for query '{}' with params {}", queryName, params, ex);
            }
        }
    }

    /**
     * Retrieves an API response for a given query name.
     *
     * @param queryName The name of the query.
     * @return The API response.
     * @throws org.nanopub.extra.services.FailedApiCallException If the API call fails.
     */
    public static ApiResponse get(String queryName) throws FailedApiCallException {
        return get(queryName, new HashMap<>());
    }

    /**
     * Retrieves an API response for a given query name and a single parameter.
     *
     * @param queryName  The name of the query.
     * @param paramKey   The key of the parameter.
     * @param paramValue The value of the parameter.
     * @return The API response.
     * @throws org.nanopub.extra.services.FailedApiCallException If the API call fails.
     */
    public static ApiResponse get(String queryName, String paramKey, String paramValue) throws FailedApiCallException {
        Map<String, String> params = new HashMap<>();
        params.put(paramKey, paramValue);
        return get(queryName, params);
    }

    /**
     * Retrieves an API response for a given query name and parameters.
     *
     * @param queryName The name of the query.
     * @param params    The parameters for the query.
     * @return The API response.
     * @throws org.nanopub.extra.services.FailedApiCallException If the API call fails.
     */
    public static ApiResponse get(String queryName, Map<String, String> params) throws FailedApiCallException {
        String queryId;
        if (queryName.matches("^RA[A-Za-z0-9-_]{43}/.*$")) {
            queryId = queryName;
        } else if (queryIds.containsKey(queryName)) {
            queryId = queryIds.get(queryName);
        } else {
            throw new IllegalArgumentException("Query name not known: " + queryName);
        }
        return QueryAccess.get(queryId, params);
    }

    /**
     * Retrieves the latest version ID of a given nanopublication.
     *
     * @param nanopubId The ID of the nanopublication.
     * @return The latest version ID.
     */
    public static String getLatestVersionId(String nanopubId) {
        long currentTime = System.currentTimeMillis();
        if (!latestVersionMap.containsKey(nanopubId) || currentTime - latestVersionMap.get(nanopubId).getLeft() > 1000 * 60) {
            // Re-fetch if existing value is older than 1 minute
            Map<String, String> params = new HashMap<>();
            params.put("np", nanopubId);
            try {
                ApiResponse r = get("get-latest-version-of-np", params);
                if (r.getData().size() != 1) return nanopubId;
                String l = r.getData().get(0).get("latest");
                latestVersionMap.put(nanopubId, Pair.of(currentTime, l));
            } catch (Exception ex) {
                logger.error("Error while getting latest version of nanopub '{}'", nanopubId, ex);
                return nanopubId;
            }
        }
        return latestVersionMap.get(nanopubId).getRight();
    }

    /**
     * Extracts the query ID from a given query IRI.
     *
     * @param queryIri The query IRI.
     * @return The query ID, or null if the IRI is invalid.
     */
    public static String getQueryId(IRI queryIri) {
        if (queryIri == null) return null;
        if (!queryIri.stringValue().matches(queryIriPattern)) return null;
        return queryIri.stringValue().replaceFirst(queryIriPattern, "$2/$3");
    }

    /**
     * Retrieves the query ID for a given query name.
     *
     * @param queryName The name of the query.
     * @return The query ID, or null if the query name is unknown.
     */
    public static String getQueryId(String queryName) {
        return queryIds.get(queryName);
    }

    /**
     * Extracts the query name from a given query IRI.
     *
     * @param queryIri The query IRI.
     * @return The query name, or null if the IRI is invalid.
     */
    public static String getQueryName(IRI queryIri) {
        if (queryIri == null) return null;
        if (!queryIri.stringValue().matches(queryIriPattern)) return null;
        return queryIri.stringValue().replaceFirst(queryIriPattern, "$3");
    }

}

1	package com.knowledgepixels.nanodash;
2
3	import org.apache.commons.lang3.tuple.Pair;
4	import org.eclipse.rdf4j.model.IRI;
5	import org.nanopub.extra.services.ApiResponse;
6	import org.nanopub.extra.services.FailedApiCallException;
7	import org.nanopub.extra.services.QueryAccess;
8	import org.slf4j.Logger;
9	import org.slf4j.LoggerFactory;
10
11	import java.util.HashMap;
12	import java.util.Map;
13	import java.util.concurrent.ConcurrentHashMap;
14	import java.util.concurrent.ConcurrentMap;
15
16	/**
17	* Utility class for accessing and managing API queries.
18	* Provides methods to retrieve query results, manage query IDs, and fetch the latest versions of nanopublications.
19	*/
20	public class QueryApiAccess {
21
22	private QueryApiAccess() {
23	} // no instances allowed
24
25	private static ConcurrentMap<String, String> queryIds = new ConcurrentHashMap<>();	4✔
26	private static final Logger logger = LoggerFactory.getLogger(QueryApiAccess.class);	3✔
27
28	private static ConcurrentMap<String, Pair<Long, String>> latestVersionMap = new ConcurrentHashMap<>();	4✔
29
30	private static final String queryIriPattern = "^(.*[^A-Za-z0-9-_])(RA[A-Za-z0-9-_]{43})[/#]([^/#]+)$";
31
32	static {
33	// TODO Load this dynamically somehow at some point:
34	load("RAe-oA5eSmkCXCALZ99-0k4imnlI74KPqURfhHOmnzo6A/get-latest-nanopubs-from-pubkeys");	2✔
35	load("RAuy4N1h4vZ1wgBUMvTiWw2y_Y0_5oFYRTwdq-xj2qqNM/get-latest-nanopubs-from-userid");	2✔
36	load("RAZbyFSenuKSRMLGlRfrbeu6vQ6g2IEECYZ2zSGcIBIhQ/get-accepted-nanopubs-by-author");	2✔
37	load("RAiCBvPL2hRGzI8g5L68O-C9yEXryC_vG35GdEm5jtH_s/get-user-stats-from-pubkeys"); // Deactivated for now...	2✔
38	load("RA3U23LL3xbNwsu92fAqsKb0kagOud4f9TlRQq3evNJck/get-user-stats-from-userid"); // Deactivated for now...	2✔
39	load("RAcNvmEiUNUb2a7O4fwRvy2x2BCN640AC880fTzFworr8/get-top-creators-last30d");	2✔
40	load("RAmhy4KQe6I80bA2Da4JziYyKBoXuXIzqo57GDSVgLfDg/get-top-authors");	2✔
41	load("RA7oUCHG8TEjVQpGTUN5sfu3_IQmza3aSBSCxfJdBc3Rs/get-most-recent-nanopubs");	2✔
42	load("RA52cg2OzJucmpCb7KSKTgfPV5HKIjsFcmww_rxb7v5zU/get-latest-accepted");	2✔
43	load("RAPGhXDRzeGu-Qk0AkjleEtxMxqAvJ-dZn7985gzAbyhs/get-publisher-version");	2✔
44	load("RAvL7pe2ppsfq4mVWTdJjssYGsjrmliNd_sZO2ytLvg1Y/get-most-used-templates-last30d");	2✔
45	load("RANn4Mu8r8bqJA9KJMGXTQAEGAEvtNKGFsuhRIC6BRIOo/get-latest-nanopubs-by-type");	2✔
46	load("RAiRsB2YywxjsBMkVRTREJBooXhf2ZOHoUs5lxciEl37I/get-latest-version-of-np");	2✔
47	load("RA0aZxyh_I0rCJyBepXOWC2tGdI5YYHORFCC-qBR8xHZA/get-all-user-intros");	2✔
48	load("RA-tlMmQA7iT2wR2aS3PlONrepX7vdXbkzeWluea7AECg/get-suggested-templates-to-get-started");	2✔
49	load("RAtIndAeo8zYnEvTjFRaHD2AlenvkJHlw6P52JWR_l5dQ/get-type-overview-last-12-months");	2✔
50	load("RAn3agwsH2yk-8132RJApGYxdPSHHCXDAIYiCaSBBo6tg/get-approved-nanopubs");	2✔
51	load("RAz1ogtMxSTKSOYwHAfD5M3Y-vd1vd46OZta_vvbqh8kY/find-uri-references");	2✔
52	load("RAE35dYJQlpnqim7VeKuu07E9I1LQUZpkdYQR4RvU3KMU/get-nanopubs-by-type");	2✔
53	load("RALZXWg5lZoJoQ0VHL5mpDgNxYpqU6FoDLWGp4rs8A6b8/get-introducing-nanopub");	2✔
54	load("RAWruhiSmyzgZhVRs8QY8YQPAgHzTfl7anxII1de-yaCs/fulltext-search-on-labels");	2✔
55	load("RAVEmFh3d6qonTFQ5S9SVqXZh0prrH1YLhSSs0dJvyvpM/find-things");	2✔
56	load("RAjt1H9rCSr6A9VGzlhye00zPdH69JdGc3kd_2VjDmzVg/get-instances");	2✔
57	load("RAH06iUwnvj_pRARY15ayJAY5tuJau3rCvHhPPhe49fVI/get-classes-for-thing");	2✔
58	load("RAJStXEm1wZcg34ZLPqe00VPSzIVCwC2rrxdj_JR8v5DY/find-referencing-nanopubs"); // not yet used...	2✔
59	load("RAtftxAXJubB4rlm9fOvvHNVIkXvWQLC6Ag_MiV7HL0ow/get-labels-for-thing"); // not yet used...	2✔
60	load("RARtWHRzNY5hh31X2VB5eOCJAdp9Cjv4CakA0Idqz69MI/get-templates-with-uri");	2✔
61	load("RAWH0fe1RCpoOgaJE1B2qfTzzdTiBUUK7iIk6l7Zll9mg/get-newer-versions-of-np");	2✔
62	load("RAQqjXQYlxYQeI4Y3UQy9OrD5Jx1E3PJ8KwKKQlWbiYSw/get-queries");	2✔
63	load("RAzXDzCHoZmJITgYYquLwDDkSyNf3eKKQz9NfQPYB1cyE/get-latest-thing-nanopub");	2✔
64	load("RAnpimW7SPwaum2fefdS6_jpzYxcTRGjE-pmgNTL_BBJU/get-projects");	2✔
65	load("RAJmZoM0xCGE8OL6EgmQBOd1M58ggNkwZ0IUqHOAPRfvE/get-parts");	2✔
66	load("RA6bgrU3Ezfg5VAiLru0BFYHaSj6vZU6jJTscxNl8Wqvc/get-assertion-templates");	2✔
67	load("RA4bt3MQRnEPC2nSsdbCJc74wT-e1w68dSCpYVyvG0274/get-provenance-templates");	2✔
68	load("RAMcdiJpvvk8424AJIH1jsDUQVcPYOLRw0DNnZt_ND_LQ/get-pubinfo-templates");	2✔
69	}	1✔
70
71	/**
72	* Loads a query ID into the queryIds map.
73	*
74	* @param queryId The query ID to load.
75	*/
76	static void load(String queryId) {
77	queryIds.put(queryId.substring(46), queryId);	7✔
78	}	1✔
79
80	/**
81	* Forces the retrieval of an API response for a given query name and parameters.
82	* Retries until a valid response is received.
83	*
84	* @param queryName The name of the query.
85	* @return The API response.
86	*/
87	public static ApiResponse forcedGet(String queryName) {
88	return forcedGet(queryName, new HashMap<>());	6✔
89	}
90
91	/**
92	* Forces the retrieval of an API response for a given query name and parameters.
93	* Retries until a valid response is received.
94	*
95	* @param queryName The name of the query.
96	* @param params The parameters for the query.
97	* @return The API response.
98	*/
99	public static ApiResponse forcedGet(String queryName, Map<String, String> params) {
100	while (true) {
101	ApiResponse resp = null;	2✔
102	try {
103	resp = QueryApiAccess.get(queryName, params);	4✔
104	} catch (Exception ex) {	1✔
105	// TODO We should be more specific about which exceptions we catch here
106	// and generally improve this, as this could hang forever.
107	logger.error("Error while forcing API get for query '{}' with params {}", queryName, params, ex);	17✔
108	}	1✔
109	if (resp != null) return resp;	4✔
110	try {
111	Thread.sleep(100);	2✔
112	} catch (InterruptedException ex) {	×
113	logger.error("Interrupted while forcing API get for query '{}' with params {}", queryName, params, ex);	×
114	}	1✔
115	}	1✔
116	}
117
118	/**
119	* Retrieves an API response for a given query name.
120	*
121	* @param queryName The name of the query.
122	* @return The API response.
123	* @throws org.nanopub.extra.services.FailedApiCallException If the API call fails.
124	*/
125	public static ApiResponse get(String queryName) throws FailedApiCallException {
126	return get(queryName, new HashMap<>());	6✔
127	}
128
129	/**
130	* Retrieves an API response for a given query name and a single parameter.
131	*
132	* @param queryName The name of the query.
133	* @param paramKey The key of the parameter.
134	* @param paramValue The value of the parameter.
135	* @return The API response.
136	* @throws org.nanopub.extra.services.FailedApiCallException If the API call fails.
137	*/
138	public static ApiResponse get(String queryName, String paramKey, String paramValue) throws FailedApiCallException {
139	Map<String, String> params = new HashMap<>();	×
140	params.put(paramKey, paramValue);	×
141	return get(queryName, params);	×
142	}
143
144	/**
145	* Retrieves an API response for a given query name and parameters.
146	*
147	* @param queryName The name of the query.
148	* @param params The parameters for the query.
149	* @return The API response.
150	* @throws org.nanopub.extra.services.FailedApiCallException If the API call fails.
151	*/
152	public static ApiResponse get(String queryName, Map<String, String> params) throws FailedApiCallException {
153	String queryId;
154	if (queryName.matches("^RA[A-Za-z0-9-_]{43}/.*$")) {	4✔
155	queryId = queryName;	3✔
156	} else if (queryIds.containsKey(queryName)) {	4✔
157	queryId = queryIds.get(queryName);	6✔
158	} else {
159	throw new IllegalArgumentException("Query name not known: " + queryName);	6✔
160	}
161	return QueryAccess.get(queryId, params);	4✔
162	}
163
164	/**
165	* Retrieves the latest version ID of a given nanopublication.
166	*
167	* @param nanopubId The ID of the nanopublication.
168	* @return The latest version ID.
169	*/
170	public static String getLatestVersionId(String nanopubId) {
171	long currentTime = System.currentTimeMillis();	2✔
172	if (!latestVersionMap.containsKey(nanopubId) \|\| currentTime - latestVersionMap.get(nanopubId).getLeft() > 1000 * 60) {	4!
173	// Re-fetch if existing value is older than 1 minute
174	Map<String, String> params = new HashMap<>();	4✔
175	params.put("np", nanopubId);	5✔
176	try {
177	ApiResponse r = get("get-latest-version-of-np", params);	4✔
178	if (r.getData().size() != 1) return nanopubId;	5!
179	String l = r.getData().get(0).get("latest");	8✔
180	latestVersionMap.put(nanopubId, Pair.of(currentTime, l));	8✔
181	} catch (Exception ex) {	×
182	logger.error("Error while getting latest version of nanopub '{}'", nanopubId, ex);	×
183	return nanopubId;	×
184	}	1✔
185	}
186	return latestVersionMap.get(nanopubId).getRight();	7✔
187	}
188
189	/**
190	* Extracts the query ID from a given query IRI.
191	*
192	* @param queryIri The query IRI.
193	* @return The query ID, or null if the IRI is invalid.
194	*/
195	public static String getQueryId(IRI queryIri) {
196	if (queryIri == null) return null;	×
197	if (!queryIri.stringValue().matches(queryIriPattern)) return null;	×
198	return queryIri.stringValue().replaceFirst(queryIriPattern, "$2/$3");	×
199	}
200
201	/**
202	* Retrieves the query ID for a given query name.
203	*
204	* @param queryName The name of the query.
205	* @return The query ID, or null if the query name is unknown.
206	*/
207	public static String getQueryId(String queryName) {
208	return queryIds.get(queryName);	5✔
209	}
210
211	/**
212	* Extracts the query name from a given query IRI.
213	*
214	* @param queryIri The query IRI.
215	* @return The query name, or null if the IRI is invalid.
216	*/
217	public static String getQueryName(IRI queryIri) {
218	if (queryIri == null) return null;	4✔
219	if (!queryIri.stringValue().matches(queryIriPattern)) return null;	7✔
220	return queryIri.stringValue().replaceFirst(queryIriPattern, "$3");	6✔
221	}
222
223	}

knowledgepixels / nanodash / 17380144000

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