18155160356

Committed 01 Oct 2025 07:42AM UTC coverage: 13.788% (-0.03%) from 13.817%

Build # 18155160356

Build Type

push

github

Committed by

ashleycaselli

Commit Message

docs: add missing or update Javadoc annotations

Run Details

445 of 4084 branches covered (10.9%)

Branch coverage included in aggregate %.

1155 of 7520 relevant lines covered (15.36%)

0.69 hits per line

Source File
Press 'n' to go to next uncovered line, 'b' for previous

82.52

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.*;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

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("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("RAr27GmRUKQmvPbfmB34N9l9lX-xYK7nQhvOMbQCk3byI/get-latest-users");
        load("RAYNg6rfvXIVvJY2u8oS0EEjxnVvimLLVZG1rOar_nWIY/get-most-recent-nanopubs");
        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("RActSoHqt-TlpCOldqLb9skfMioVxHzCZUYaNEM06FTsY/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("RAyMrQ89RECTi9gZK5q7gjL1wKTiP8StkLy0NIkkCiyew/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("RAIn9NTsWE0qrpKiK3nOmZRXVzwv0qnfbm7dR_CUnp4aA/get-newer-versions-of-np");
        load("RAQqjXQYlxYQeI4Y3UQy9OrD5Jx1E3PJ8KwKKQlWbiYSw/get-queries");
        load("RAzXDzCHoZmJITgYYquLwDDkSyNf3eKKQz9NfQPYB1cyE/get-latest-thing-nanopub");
        load("RAnpimW7SPwaum2fefdS6_jpzYxcTRGjE-pmgNTL_BBJU/get-projects");
        load("RApiw7Z0NeP3RaLiqX6Q7Ml5CfEWbt-PysUbMNljuiLJw/get-owners");
        load("RASyFJyADTtG-l_Qe3a5PE_e2yUJR-PydXfkZjjrBuV7U/get-members");
        load("RAlPzIqHJsPt33WuPNBIyPDr8KC7htHO9UYvSuYOfTjwo/get-spaces");
        load("RAJmZoM0xCGE8OL6EgmQBOd1M58ggNkwZ0IUqHOAPRfvE/get-parts");
        load("RA6bgrU3Ezfg5VAiLru0BFYHaSj6vZU6jJTscxNl8Wqvc/get-assertion-templates");
        load("RA4bt3MQRnEPC2nSsdbCJc74wT-e1w68dSCpYVyvG0274/get-provenance-templates");
        load("RAMcdiJpvvk8424AJIH1jsDUQVcPYOLRw0DNnZt_ND_LQ/get-pubinfo-templates");
        load("RAOpebLWcp0G6D9U8ZhfYGOkz-kObkytDsM6rCQlIi_j0/get-admins");
        load("RA_Xf7mfC2PAohGYktJEXjkbzxPhkfX4DE1bQKFqkxrRg/get-space-members");
        load("RAbq1a1FwRFAZPDde3Sy4GqNUQ2TmaKOWLydJPOyCKc0w/get-filtered-nanopub-list");
        load("RA_F6C2DtlL4EXSF2vzU1KLVUiRLjPAM-r1Wy32JIeSYI/get-pinned-templates");
        load("RAH5jJUo8ukFkPP1xghveSNPze3pmSK69zri5PPM6HEbg/get-pinned-queries");
        load("RALlWmTd48iZxMSxUxIaM24NwiSngygwKcK4_sl6bS2jo/get-space-member-roles");
        load("RA5dahGhH4UOqGYMFbh17I7iUWTd5llmedpv0TvVgKNwg/get-views-for-space");
    }

    /**
     * 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 queryRef The query reference
     * @return The API response.
     */
    public static ApiResponse forcedGet(QueryRef queryRef) {
        while (true) {
            ApiResponse resp = null;
            try {
                resp = QueryApiAccess.get(queryRef);
            } 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 {}", queryRef, ex);
            }
            if (resp != null) return resp;
            try {
                Thread.sleep(100);
            } catch (InterruptedException ex) {
                logger.error("Interrupted while forcing API get for query {}", queryRef, ex);
            }
        }
    }

    /**
     * Retrieves an API response for a given query reference.
     *
     * @param queryRef The query reference
     * @return The API response.
     * @throws org.nanopub.extra.services.FailedApiCallException         If the API call fails.
     * @throws org.nanopub.extra.services.APINotReachableException       If the API is not reachable.
     * @throws org.nanopub.extra.services.NotEnoughAPIInstancesException If there are not enough API instances.
     */
    public static ApiResponse get(QueryRef queryRef) throws FailedApiCallException, APINotReachableException, NotEnoughAPIInstancesException {
        if (queryRef.getName().matches("^RA[A-Za-z0-9-_]{43}/.*$")) {
            // All good
        } else if (queryIds.containsKey(queryRef.getName())) {
            queryRef = new QueryRef(queryIds.get(queryRef.getName()), queryRef.getParams());
        } else {
            throw new IllegalArgumentException("Query name not known: " + queryRef.getName());
        }
        return QueryAccess.get(queryRef);
    }

    /**
     * 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
            try {
                ApiResponse r = get(new QueryRef("get-latest-version-of-np", "np", nanopubId));
                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.*;
6	import org.slf4j.Logger;
7	import org.slf4j.LoggerFactory;
8
9	import java.util.concurrent.ConcurrentHashMap;
10	import java.util.concurrent.ConcurrentMap;
11
12	/**
13	* Utility class for accessing and managing API queries.
14	* Provides methods to retrieve query results, manage query IDs, and fetch the latest versions of nanopublications.
15	*/
16	public class QueryApiAccess {
17
18	private QueryApiAccess() {
19	} // no instances allowed
20
21	private static ConcurrentMap<String, String> queryIds = new ConcurrentHashMap<>();	4✔
22	private static final Logger logger = LoggerFactory.getLogger(QueryApiAccess.class);	3✔
23
24	private static ConcurrentMap<String, Pair<Long, String>> latestVersionMap = new ConcurrentHashMap<>();	4✔
25
26	private static final String queryIriPattern = "^(.*[^A-Za-z0-9-_])(RA[A-Za-z0-9-_]{43})[/#]([^/#]+)$";
27
28	static {
29	// TODO Load this dynamically somehow at some point:
30	load("RAe-oA5eSmkCXCALZ99-0k4imnlI74KPqURfhHOmnzo6A/get-latest-nanopubs-from-pubkeys");	2✔
31	load("RAuy4N1h4vZ1wgBUMvTiWw2y_Y0_5oFYRTwdq-xj2qqNM/get-latest-nanopubs-from-userid");	2✔
32	load("RAiCBvPL2hRGzI8g5L68O-C9yEXryC_vG35GdEm5jtH_s/get-user-stats-from-pubkeys"); // Deactivated for now...	2✔
33	load("RA3U23LL3xbNwsu92fAqsKb0kagOud4f9TlRQq3evNJck/get-user-stats-from-userid"); // Deactivated for now...	2✔
34	load("RAcNvmEiUNUb2a7O4fwRvy2x2BCN640AC880fTzFworr8/get-top-creators-last30d");	2✔
35	load("RAr27GmRUKQmvPbfmB34N9l9lX-xYK7nQhvOMbQCk3byI/get-latest-users");	2✔
36	load("RAYNg6rfvXIVvJY2u8oS0EEjxnVvimLLVZG1rOar_nWIY/get-most-recent-nanopubs");	2✔
37	load("RAPGhXDRzeGu-Qk0AkjleEtxMxqAvJ-dZn7985gzAbyhs/get-publisher-version");	2✔
38	load("RAvL7pe2ppsfq4mVWTdJjssYGsjrmliNd_sZO2ytLvg1Y/get-most-used-templates-last30d");	2✔
39	load("RANn4Mu8r8bqJA9KJMGXTQAEGAEvtNKGFsuhRIC6BRIOo/get-latest-nanopubs-by-type");	2✔
40	load("RAiRsB2YywxjsBMkVRTREJBooXhf2ZOHoUs5lxciEl37I/get-latest-version-of-np");	2✔
41	load("RA0aZxyh_I0rCJyBepXOWC2tGdI5YYHORFCC-qBR8xHZA/get-all-user-intros");	2✔
42	load("RA-tlMmQA7iT2wR2aS3PlONrepX7vdXbkzeWluea7AECg/get-suggested-templates-to-get-started");	2✔
43	load("RActSoHqt-TlpCOldqLb9skfMioVxHzCZUYaNEM06FTsY/get-type-overview-last-12-months");	2✔
44	load("RAn3agwsH2yk-8132RJApGYxdPSHHCXDAIYiCaSBBo6tg/get-approved-nanopubs");	2✔
45	load("RAz1ogtMxSTKSOYwHAfD5M3Y-vd1vd46OZta_vvbqh8kY/find-uri-references");	2✔
46	load("RAE35dYJQlpnqim7VeKuu07E9I1LQUZpkdYQR4RvU3KMU/get-nanopubs-by-type");	2✔
47	load("RALZXWg5lZoJoQ0VHL5mpDgNxYpqU6FoDLWGp4rs8A6b8/get-introducing-nanopub");	2✔
48	load("RAWruhiSmyzgZhVRs8QY8YQPAgHzTfl7anxII1de-yaCs/fulltext-search-on-labels");	2✔
49	load("RAyMrQ89RECTi9gZK5q7gjL1wKTiP8StkLy0NIkkCiyew/find-things");	2✔
50	load("RAjt1H9rCSr6A9VGzlhye00zPdH69JdGc3kd_2VjDmzVg/get-instances");	2✔
51	load("RAH06iUwnvj_pRARY15ayJAY5tuJau3rCvHhPPhe49fVI/get-classes-for-thing");	2✔
52	load("RAJStXEm1wZcg34ZLPqe00VPSzIVCwC2rrxdj_JR8v5DY/find-referencing-nanopubs"); // not yet used...	2✔
53	load("RAtftxAXJubB4rlm9fOvvHNVIkXvWQLC6Ag_MiV7HL0ow/get-labels-for-thing"); // not yet used...	2✔
54	load("RARtWHRzNY5hh31X2VB5eOCJAdp9Cjv4CakA0Idqz69MI/get-templates-with-uri");	2✔
55	load("RAIn9NTsWE0qrpKiK3nOmZRXVzwv0qnfbm7dR_CUnp4aA/get-newer-versions-of-np");	2✔
56	load("RAQqjXQYlxYQeI4Y3UQy9OrD5Jx1E3PJ8KwKKQlWbiYSw/get-queries");	2✔
57	load("RAzXDzCHoZmJITgYYquLwDDkSyNf3eKKQz9NfQPYB1cyE/get-latest-thing-nanopub");	2✔
58	load("RAnpimW7SPwaum2fefdS6_jpzYxcTRGjE-pmgNTL_BBJU/get-projects");	2✔
59	load("RApiw7Z0NeP3RaLiqX6Q7Ml5CfEWbt-PysUbMNljuiLJw/get-owners");	2✔
60	load("RASyFJyADTtG-l_Qe3a5PE_e2yUJR-PydXfkZjjrBuV7U/get-members");	2✔
61	load("RAlPzIqHJsPt33WuPNBIyPDr8KC7htHO9UYvSuYOfTjwo/get-spaces");	2✔
62	load("RAJmZoM0xCGE8OL6EgmQBOd1M58ggNkwZ0IUqHOAPRfvE/get-parts");	2✔
63	load("RA6bgrU3Ezfg5VAiLru0BFYHaSj6vZU6jJTscxNl8Wqvc/get-assertion-templates");	2✔
64	load("RA4bt3MQRnEPC2nSsdbCJc74wT-e1w68dSCpYVyvG0274/get-provenance-templates");	2✔
65	load("RAMcdiJpvvk8424AJIH1jsDUQVcPYOLRw0DNnZt_ND_LQ/get-pubinfo-templates");	2✔
66	load("RAOpebLWcp0G6D9U8ZhfYGOkz-kObkytDsM6rCQlIi_j0/get-admins");	2✔
67	load("RA_Xf7mfC2PAohGYktJEXjkbzxPhkfX4DE1bQKFqkxrRg/get-space-members");	2✔
68	load("RAbq1a1FwRFAZPDde3Sy4GqNUQ2TmaKOWLydJPOyCKc0w/get-filtered-nanopub-list");	2✔
69	load("RA_F6C2DtlL4EXSF2vzU1KLVUiRLjPAM-r1Wy32JIeSYI/get-pinned-templates");	2✔
70	load("RAH5jJUo8ukFkPP1xghveSNPze3pmSK69zri5PPM6HEbg/get-pinned-queries");	2✔
71	load("RALlWmTd48iZxMSxUxIaM24NwiSngygwKcK4_sl6bS2jo/get-space-member-roles");	2✔
72	load("RA5dahGhH4UOqGYMFbh17I7iUWTd5llmedpv0TvVgKNwg/get-views-for-space");	2✔
73	}	1✔
74
75	/**
76	* Loads a query ID into the queryIds map.
77	*
78	* @param queryId The query ID to load.
79	*/
80	static void load(String queryId) {
81	queryIds.put(queryId.substring(46), queryId);	7✔
82	}	1✔
83
84	/**
85	* Forces the retrieval of an API response for a given query name and parameters.
86	* Retries until a valid response is received.
87	*
88	* @param queryRef The query reference
89	* @return The API response.
90	*/
91	public static ApiResponse forcedGet(QueryRef queryRef) {
92	while (true) {
93	ApiResponse resp = null;	2✔
94	try {
95	resp = QueryApiAccess.get(queryRef);	3✔
96	} catch (Exception ex) {	×
97	// TODO We should be more specific about which exceptions we catch here
98	// and generally improve this, as this could hang forever.
99	logger.error("Error while forcing API get for query {}", queryRef, ex);	×
100	}	1✔
101	if (resp != null) return resp;	4✔
102	try {
103	Thread.sleep(100);	2✔
104	} catch (InterruptedException ex) {	×
105	logger.error("Interrupted while forcing API get for query {}", queryRef, ex);	×
106	}	1✔
107	}	1✔
108	}
109
110	/**
111	* Retrieves an API response for a given query reference.
112	*
113	* @param queryRef The query reference
114	* @return The API response.
115	* @throws org.nanopub.extra.services.FailedApiCallException If the API call fails.
116	* @throws org.nanopub.extra.services.APINotReachableException If the API is not reachable.
117	* @throws org.nanopub.extra.services.NotEnoughAPIInstancesException If there are not enough API instances.
118	*/
119	public static ApiResponse get(QueryRef queryRef) throws FailedApiCallException, APINotReachableException, NotEnoughAPIInstancesException {
120	if (queryRef.getName().matches("^RA[A-Za-z0-9-_]{43}/.*$")) {	6✔
121	// All good
122	} else if (queryIds.containsKey(queryRef.getName())) {	5✔
123	queryRef = new QueryRef(queryIds.get(queryRef.getName()), queryRef.getParams());	12✔
124	} else {
125	throw new IllegalArgumentException("Query name not known: " + queryRef.getName());	7✔
126	}
127	return QueryAccess.get(queryRef);	3✔
128	}
129
130	/**
131	* Retrieves the latest version ID of a given nanopublication.
132	*
133	* @param nanopubId The ID of the nanopublication.
134	* @return The latest version ID.
135	*/
136	public static String getLatestVersionId(String nanopubId) {
137	long currentTime = System.currentTimeMillis();	2✔
138	if (!latestVersionMap.containsKey(nanopubId) \|\| currentTime - latestVersionMap.get(nanopubId).getLeft() > 1000 * 60) {	4!
139	// Re-fetch if existing value is older than 1 minute
140	try {
141	ApiResponse r = get(new QueryRef("get-latest-version-of-np", "np", nanopubId));	8✔
142	if (r.getData().size() != 1) return nanopubId;	5!
143	String l = r.getData().get(0).get("latest");	8✔
144	latestVersionMap.put(nanopubId, Pair.of(currentTime, l));	8✔
145	} catch (Exception ex) {	×
146	logger.error("Error while getting latest version of nanopub '{}'", nanopubId, ex);	×
147	return nanopubId;	×
148	}	1✔
149	}
150	return latestVersionMap.get(nanopubId).getRight();	7✔
151	}
152
153	/**
154	* Extracts the query ID from a given query IRI.
155	*
156	* @param queryIri The query IRI.
157	* @return The query ID, or null if the IRI is invalid.
158	*/
159	public static String getQueryId(IRI queryIri) {
160	if (queryIri == null) return null;	×
161	if (!queryIri.stringValue().matches(queryIriPattern)) return null;	×
162	return queryIri.stringValue().replaceFirst(queryIriPattern, "$2/$3");	×
163	}
164
165	/**
166	* Retrieves the query ID for a given query name.
167	*
168	* @param queryName The name of the query.
169	* @return The query ID, or null if the query name is unknown.
170	*/
171	public static String getQueryId(String queryName) {
172	return queryIds.get(queryName);	5✔
173	}
174
175	/**
176	* Extracts the query name from a given query IRI.
177	*
178	* @param queryIri The query IRI.
179	* @return The query name, or null if the IRI is invalid.
180	*/
181	public static String getQueryName(IRI queryIri) {
182	if (queryIri == null) return null;	4✔
183	if (!queryIri.stringValue().matches(queryIriPattern)) return null;	7✔
184	return queryIri.stringValue().replaceFirst(queryIriPattern, "$3");	6✔
185	}
186
187	}

knowledgepixels / nanodash / 18155160356

Source File Press 'n' to go to next uncovered line, 'b' for previous

Source File
Press 'n' to go to next uncovered line, 'b' for previous