23541488268

Committed 25 Mar 2026 12:40PM UTC coverage: 31.704% (+1.1%) from 30.645%

Build # 23541488268

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push

github

Committed by

web-flow

Commit Message

Merge pull request #89 from knowledgepixels/perf/db-operation-improvements

perf: optimize DB operations for replication speed

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206 of 730 branches covered (28.22%)

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10.12

src/main/java/com/knowledgepixels/registry/NanopubLoader.java

package com.knowledgepixels.registry;

import com.mongodb.ErrorCategory;
import com.mongodb.MongoWriteException;
import com.mongodb.client.ClientSession;
import com.mongodb.client.MongoCursor;
import net.trustyuri.TrustyUriUtils;
import net.trustyuri.rdf.RdfModule;
import org.apache.http.Header;
import org.apache.http.HttpResponse;
import org.apache.http.client.HttpClient;
import org.apache.http.client.methods.CloseableHttpResponse;
import org.apache.http.client.methods.HttpGet;
import org.apache.http.util.EntityUtils;
import org.bson.Document;
import org.bson.types.Binary;
import org.eclipse.rdf4j.common.exception.RDF4JException;
import org.eclipse.rdf4j.rio.RDFFormat;
import org.nanopub.MalformedNanopubException;
import org.nanopub.Nanopub;
import org.nanopub.NanopubImpl;
import org.nanopub.NanopubUtils;
import org.nanopub.extra.server.GetNanopub;
import org.nanopub.jelly.JellyUtils;
import org.nanopub.jelly.MaybeNanopub;
import org.nanopub.jelly.NanopubStream;
import org.nanopub.trusty.TrustyNanopubUtils;
import org.nanopub.vocabulary.NPX;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.util.stream.Stream;

import static com.knowledgepixels.registry.RegistryDB.has;
import static com.knowledgepixels.registry.RegistryDB.insert;

public class NanopubLoader {

    private NanopubLoader() {
    }

    public final static String INTRO_TYPE = NPX.DECLARED_BY.stringValue();
    public final static String INTRO_TYPE_HASH = Utils.getHash(INTRO_TYPE);
    public final static String ENDORSE_TYPE = Utils.APPROVES_OF.stringValue();
    public final static String ENDORSE_TYPE_HASH = Utils.getHash(ENDORSE_TYPE);
    private static final Logger log = LoggerFactory.getLogger(NanopubLoader.class);

    // TODO Distinguish and support these cases:
    //      1. Simple load: load to all core lists if pubkey is "core-loaded", or load to all lists if pubkey is "full-loaded"
    //      2. Core load: load to all core lists (initialize if needed), or load to all lists if pubkey is "full-loaded"
    //      3. Full load: load to all lists (initialize if needed)

    public static void simpleLoad(ClientSession mongoSession, String nanopubId) {
        simpleLoad(mongoSession, retrieveNanopub(mongoSession, nanopubId));
    }

    public static void simpleLoad(ClientSession mongoSession, Nanopub np) {
        String pubkey = RegistryDB.getPubkey(np);
        if (pubkey == null) {
            log.info("Ignore (not signed): {}", np.getUri());
            return;
        }
        simpleLoad(mongoSession, np, pubkey);
    }

    /**
     * Loads a nanopub to the appropriate lists, using a pre-verified public key
     * to skip redundant signature verification.
     */
    public static void simpleLoad(ClientSession mongoSession, Nanopub np, String verifiedPubkey) {
        String pubkeyHash = Utils.getHash(verifiedPubkey);
        // TODO Do we need to load anything else here, into the other DB collections?
        if (has(mongoSession, "lists", new Document("pubkey", pubkeyHash).append("type", "$").append("status", "loaded"))) {
            RegistryDB.loadNanopubVerified(mongoSession, np, verifiedPubkey, pubkeyHash, "$");
        } else if (has(mongoSession, "lists", new Document("pubkey", pubkeyHash).append("type", INTRO_TYPE_HASH).append("status", "loaded"))) {
            RegistryDB.loadNanopubVerified(mongoSession, np, verifiedPubkey, pubkeyHash, INTRO_TYPE, ENDORSE_TYPE);
        } else if (!has(mongoSession, "lists", new Document("pubkey", pubkeyHash).append("type", INTRO_TYPE_HASH))) {
            // Unknown pubkey: create encountered intro list so RUN_OPTIONAL_LOAD picks it up
            try {
                insert(mongoSession, "lists", new Document("pubkey", pubkeyHash)
                        .append("type", INTRO_TYPE_HASH)
                        .append("status", EntryStatus.encountered.getValue()));
            } catch (MongoWriteException e) {
                if (e.getError().getCategory() != ErrorCategory.DUPLICATE_KEY) throw e;
            }
        }
    }

    /**
     * Retrieve Nanopubs from the peers of this Nanopub Registry.
     *
     * @param typeHash   The hash of the type of the Nanopub to retrieve.
     * @param pubkeyHash The hash of the pubkey of the Nanopub to retrieve.
     * @return A stream of MaybeNanopub objects, or an empty stream if no peer is available.
     */
    public static Stream<MaybeNanopub> retrieveNanopubsFromPeers(String typeHash, String pubkeyHash) {
        return retrieveNanopubsFromPeers(typeHash, pubkeyHash, null);
    }

    /**
     * Retrieve Nanopubs from the peers, optionally skipping ahead using checksums.
     *
     * @param typeHash        The hash of the type of the Nanopub to retrieve.
     * @param pubkeyHash      The hash of the pubkey of the Nanopub to retrieve.
     * @param afterChecksums  Comma-separated checksums for skip-ahead (geometric fallback), or null for full fetch.
     * @return A stream of MaybeNanopub objects, or an empty stream if no peer is available.
     */
    public static Stream<MaybeNanopub> retrieveNanopubsFromPeers(String typeHash, String pubkeyHash, String afterChecksums) {
        // TODO Move the code of this method to nanopub-java library.

        List<String> peerUrlsToTry = new ArrayList<>(Utils.getPeerUrls());
        Collections.shuffle(peerUrlsToTry);
        while (!peerUrlsToTry.isEmpty()) {
            String peerUrl = peerUrlsToTry.removeFirst();

            String requestUrl = peerUrl + "list/" + pubkeyHash + "/" + typeHash + ".jelly";
            if (afterChecksums != null) {
                requestUrl += "?afterChecksums=" + afterChecksums;
            }
            log.info("Request: {}", requestUrl);
            try {
                CloseableHttpResponse resp = NanopubUtils.getHttpClient().execute(new HttpGet(requestUrl));
                int httpStatus = resp.getStatusLine().getStatusCode();
                if (httpStatus < 200 || httpStatus >= 300) {
                    log.info("Request failed: {} {}", peerUrl, httpStatus);
                    EntityUtils.consumeQuietly(resp.getEntity());
                    continue;
                }
                Header nrStatus = resp.getFirstHeader("Nanopub-Registry-Status");
                if (nrStatus == null) {
                    log.info("Nanopub-Registry-Status header not found at: {}", peerUrl);
                    EntityUtils.consumeQuietly(resp.getEntity());
                    continue;
                } else if (!nrStatus.getValue().equals("ready") && !nrStatus.getValue().equals("updating")) {
                    log.info("Peer in non-ready state: {} {}", peerUrl, nrStatus.getValue());
                    EntityUtils.consumeQuietly(resp.getEntity());
                    continue;
                }
                InputStream is = resp.getEntity().getContent();
                return NanopubStream.fromByteStream(is).getAsNanopubs().onClose(() -> {
                    try {
                        resp.close();
                    } catch (IOException e) {
                        log.debug("Error closing HTTP response", e);
                    }
                });
            } catch (UnsupportedOperationException | IOException ex) {
                log.info("Request failed: ", ex);
            }
        }
        return Stream.empty();
    }

    public static Nanopub retrieveNanopub(ClientSession mongoSession, String nanopubId) {
        Nanopub np = retrieveLocalNanopub(mongoSession, nanopubId);
        int tryCount = 0;
        while (np == null) {
            if (tryCount > 10) {
                throw new RuntimeException("Could not load nanopub: " + nanopubId);
            } else if (tryCount > 0) {
                try {
                    Thread.sleep(100);
                } catch (InterruptedException ex) {
                    log.info("Thread was interrupted", ex);
                }
            }
            log.info("Loading {}", nanopubId);

            // TODO Reach out to other Nanopub Registries here:
            np = getNanopub(nanopubId);
            if (np != null) {
                RegistryDB.loadNanopub(mongoSession, np);
            } else {
                tryCount = tryCount + 1;
            }
        }
        return np;
    }

    public static Nanopub retrieveLocalNanopub(ClientSession mongoSession, String nanopubId) {
        String ac = TrustyUriUtils.getArtifactCode(nanopubId);
        MongoCursor<Document> cursor = RegistryDB.get(mongoSession, Collection.NANOPUBS.toString(), new Document("_id", ac));
        if (!cursor.hasNext()) return null;
        try {
            // Parse from Jelly, not TriG (it's faster)
            return JellyUtils.readFromDB(((Binary) cursor.next().get("jelly")).getData());
        } catch (RDF4JException | MalformedNanopubException ex) {
            log.info("Exception reading Jelly", ex);
            return null;
        }
    }

    // TODO Provide this method in nanopub-java (GetNanopub)
    private static Nanopub getNanopub(String uriOrArtifactCode) {
        List<String> peerUrls = new ArrayList<>(Utils.getPeerUrls());
        Collections.shuffle(peerUrls);
        String ac = GetNanopub.getArtifactCode(uriOrArtifactCode);
        if (!ac.startsWith(RdfModule.MODULE_ID)) {
            throw new IllegalArgumentException("Not a trusty URI of type RA");
        }
        while (!peerUrls.isEmpty()) {
            String peerUrl = peerUrls.removeFirst();
            try {
                Nanopub np = get(ac, peerUrl, NanopubUtils.getHttpClient());
                if (np != null) {
                    return np;
                }
            } catch (IOException | RDF4JException | MalformedNanopubException ex) {
                // ignore
            }
        }
        return null;
    }

    // TODO Provide this method in nanopub-java (GetNanopub)
    private static Nanopub get(String artifactCode, String registryUrl, HttpClient httpClient)
            throws IOException, RDF4JException, MalformedNanopubException {
        HttpGet get = null;
        // TODO Get in Jelly format:
        String getUrl = registryUrl + "np/" + artifactCode;
        try {
            get = new HttpGet(getUrl);
        } catch (IllegalArgumentException ex) {
            throw new IOException("invalid URL: " + getUrl);
        }
        get.setHeader("Accept", "application/trig");
        InputStream in = null;
        try {
            HttpResponse resp = httpClient.execute(get);
            if (!wasSuccessful(resp)) {
                EntityUtils.consumeQuietly(resp.getEntity());
                throw new IOException(resp.getStatusLine().toString());
            }
            in = resp.getEntity().getContent();
            Nanopub nanopub = new NanopubImpl(in, RDFFormat.TRIG);
            if (!TrustyNanopubUtils.isValidTrustyNanopub(nanopub)) {
                throw new MalformedNanopubException("Nanopub is not trusty");
            }
            return nanopub;
        } finally {
            if (in != null) in.close();
        }
    }

    private static boolean wasSuccessful(HttpResponse resp) {
        int c = resp.getStatusLine().getStatusCode();
        return c >= 200 && c < 300;
    }

}

1	package com.knowledgepixels.registry;
2
3	import com.mongodb.ErrorCategory;
4	import com.mongodb.MongoWriteException;
5	import com.mongodb.client.ClientSession;
6	import com.mongodb.client.MongoCursor;
7	import net.trustyuri.TrustyUriUtils;
8	import net.trustyuri.rdf.RdfModule;
9	import org.apache.http.Header;
10	import org.apache.http.HttpResponse;
11	import org.apache.http.client.HttpClient;
12	import org.apache.http.client.methods.CloseableHttpResponse;
13	import org.apache.http.client.methods.HttpGet;
14	import org.apache.http.util.EntityUtils;
15	import org.bson.Document;
16	import org.bson.types.Binary;
17	import org.eclipse.rdf4j.common.exception.RDF4JException;
18	import org.eclipse.rdf4j.rio.RDFFormat;
19	import org.nanopub.MalformedNanopubException;
20	import org.nanopub.Nanopub;
21	import org.nanopub.NanopubImpl;
22	import org.nanopub.NanopubUtils;
23	import org.nanopub.extra.server.GetNanopub;
24	import org.nanopub.jelly.JellyUtils;
25	import org.nanopub.jelly.MaybeNanopub;
26	import org.nanopub.jelly.NanopubStream;
27	import org.nanopub.trusty.TrustyNanopubUtils;
28	import org.nanopub.vocabulary.NPX;
29	import org.slf4j.Logger;
30	import org.slf4j.LoggerFactory;
31
32	import java.io.IOException;
33	import java.io.InputStream;
34	import java.util.ArrayList;
35	import java.util.Collections;
36	import java.util.List;
37	import java.util.stream.Stream;
38
39	import static com.knowledgepixels.registry.RegistryDB.has;
40	import static com.knowledgepixels.registry.RegistryDB.insert;
41
42	public class NanopubLoader {
43
44	private NanopubLoader() {
45	}
46
47	public final static String INTRO_TYPE = NPX.DECLARED_BY.stringValue();	9✔
48	public final static String INTRO_TYPE_HASH = Utils.getHash(INTRO_TYPE);	9✔
49	public final static String ENDORSE_TYPE = Utils.APPROVES_OF.stringValue();	9✔
50	public final static String ENDORSE_TYPE_HASH = Utils.getHash(ENDORSE_TYPE);	9✔
51	private static final Logger log = LoggerFactory.getLogger(NanopubLoader.class);	12✔
52
53	// TODO Distinguish and support these cases:
54	// 1. Simple load: load to all core lists if pubkey is "core-loaded", or load to all lists if pubkey is "full-loaded"
55	// 2. Core load: load to all core lists (initialize if needed), or load to all lists if pubkey is "full-loaded"
56	// 3. Full load: load to all lists (initialize if needed)
57
58	public static void simpleLoad(ClientSession mongoSession, String nanopubId) {
59	simpleLoad(mongoSession, retrieveNanopub(mongoSession, nanopubId));	×
60	}	×
61
62	public static void simpleLoad(ClientSession mongoSession, Nanopub np) {
63	String pubkey = RegistryDB.getPubkey(np);	×
64	if (pubkey == null) {	×
65	log.info("Ignore (not signed): {}", np.getUri());	×
66	return;	×
67	}
68	simpleLoad(mongoSession, np, pubkey);	×
69	}	×
70
71	/**
72	* Loads a nanopub to the appropriate lists, using a pre-verified public key
73	* to skip redundant signature verification.
74	*/
75	public static void simpleLoad(ClientSession mongoSession, Nanopub np, String verifiedPubkey) {
76	String pubkeyHash = Utils.getHash(verifiedPubkey);	9✔
77	// TODO Do we need to load anything else here, into the other DB collections?
78	if (has(mongoSession, "lists", new Document("pubkey", pubkeyHash).append("type", "$").append("status", "loaded"))) {	45!
79	RegistryDB.loadNanopubVerified(mongoSession, np, verifiedPubkey, pubkeyHash, "$");	×
80	} else if (has(mongoSession, "lists", new Document("pubkey", pubkeyHash).append("type", INTRO_TYPE_HASH).append("status", "loaded"))) {	45!
81	RegistryDB.loadNanopubVerified(mongoSession, np, verifiedPubkey, pubkeyHash, INTRO_TYPE, ENDORSE_TYPE);	×
82	} else if (!has(mongoSession, "lists", new Document("pubkey", pubkeyHash).append("type", INTRO_TYPE_HASH))) {	36!
83	// Unknown pubkey: create encountered intro list so RUN_OPTIONAL_LOAD picks it up
84	try {
85	insert(mongoSession, "lists", new Document("pubkey", pubkeyHash)	30✔
86	.append("type", INTRO_TYPE_HASH)	9✔
87	.append("status", EntryStatus.encountered.getValue()));	6✔
88	} catch (MongoWriteException e) {	×
89	if (e.getError().getCategory() != ErrorCategory.DUPLICATE_KEY) throw e;	×
90	}	3✔
91	}
92	}	3✔
93
94	/**
95	* Retrieve Nanopubs from the peers of this Nanopub Registry.
96	*
97	* @param typeHash The hash of the type of the Nanopub to retrieve.
98	* @param pubkeyHash The hash of the pubkey of the Nanopub to retrieve.
99	* @return A stream of MaybeNanopub objects, or an empty stream if no peer is available.
100	*/
101	public static Stream<MaybeNanopub> retrieveNanopubsFromPeers(String typeHash, String pubkeyHash) {
102	return retrieveNanopubsFromPeers(typeHash, pubkeyHash, null);	×
103	}
104
105	/**
106	* Retrieve Nanopubs from the peers, optionally skipping ahead using checksums.
107	*
108	* @param typeHash The hash of the type of the Nanopub to retrieve.
109	* @param pubkeyHash The hash of the pubkey of the Nanopub to retrieve.
110	* @param afterChecksums Comma-separated checksums for skip-ahead (geometric fallback), or null for full fetch.
111	* @return A stream of MaybeNanopub objects, or an empty stream if no peer is available.
112	*/
113	public static Stream<MaybeNanopub> retrieveNanopubsFromPeers(String typeHash, String pubkeyHash, String afterChecksums) {
114	// TODO Move the code of this method to nanopub-java library.
115
116	List<String> peerUrlsToTry = new ArrayList<>(Utils.getPeerUrls());	×
117	Collections.shuffle(peerUrlsToTry);	×
118	while (!peerUrlsToTry.isEmpty()) {	×
119	String peerUrl = peerUrlsToTry.removeFirst();	×
120
121	String requestUrl = peerUrl + "list/" + pubkeyHash + "/" + typeHash + ".jelly";	×
122	if (afterChecksums != null) {	×
123	requestUrl += "?afterChecksums=" + afterChecksums;	×
124	}
125	log.info("Request: {}", requestUrl);	×
126	try {
127	CloseableHttpResponse resp = NanopubUtils.getHttpClient().execute(new HttpGet(requestUrl));	×
128	int httpStatus = resp.getStatusLine().getStatusCode();	×
129	if (httpStatus < 200 \|\| httpStatus >= 300) {	×
130	log.info("Request failed: {} {}", peerUrl, httpStatus);	×
131	EntityUtils.consumeQuietly(resp.getEntity());	×
132	continue;	×
133	}
134	Header nrStatus = resp.getFirstHeader("Nanopub-Registry-Status");	×
135	if (nrStatus == null) {	×
136	log.info("Nanopub-Registry-Status header not found at: {}", peerUrl);	×
137	EntityUtils.consumeQuietly(resp.getEntity());	×
138	continue;	×
139	} else if (!nrStatus.getValue().equals("ready") && !nrStatus.getValue().equals("updating")) {	×
140	log.info("Peer in non-ready state: {} {}", peerUrl, nrStatus.getValue());	×
141	EntityUtils.consumeQuietly(resp.getEntity());	×
142	continue;	×
143	}
144	InputStream is = resp.getEntity().getContent();	×
145	return NanopubStream.fromByteStream(is).getAsNanopubs().onClose(() -> {	×
146	try {
147	resp.close();	×
148	} catch (IOException e) {	×
149	log.debug("Error closing HTTP response", e);	×
150	}	×
151	});	×
152	} catch (UnsupportedOperationException \| IOException ex) {	×
153	log.info("Request failed: ", ex);	×
154	}
155	}	×
156	return Stream.empty();	×
157	}
158
159	public static Nanopub retrieveNanopub(ClientSession mongoSession, String nanopubId) {
160	Nanopub np = retrieveLocalNanopub(mongoSession, nanopubId);	×
161	int tryCount = 0;	×
162	while (np == null) {	×
163	if (tryCount > 10) {	×
164	throw new RuntimeException("Could not load nanopub: " + nanopubId);	×
165	} else if (tryCount > 0) {	×
166	try {
167	Thread.sleep(100);	×
168	} catch (InterruptedException ex) {	×
169	log.info("Thread was interrupted", ex);	×
170	}	×
171	}
172	log.info("Loading {}", nanopubId);	×
173
174	// TODO Reach out to other Nanopub Registries here:
175	np = getNanopub(nanopubId);	×
176	if (np != null) {	×
177	RegistryDB.loadNanopub(mongoSession, np);	×
178	} else {
179	tryCount = tryCount + 1;	×
180	}
181	}
182	return np;	×
183	}
184
185	public static Nanopub retrieveLocalNanopub(ClientSession mongoSession, String nanopubId) {
186	String ac = TrustyUriUtils.getArtifactCode(nanopubId);	×
187	MongoCursor<Document> cursor = RegistryDB.get(mongoSession, Collection.NANOPUBS.toString(), new Document("_id", ac));	×
188	if (!cursor.hasNext()) return null;	×
189	try {
190	// Parse from Jelly, not TriG (it's faster)
191	return JellyUtils.readFromDB(((Binary) cursor.next().get("jelly")).getData());	×
192	} catch (RDF4JException \| MalformedNanopubException ex) {	×
193	log.info("Exception reading Jelly", ex);	×
194	return null;	×
195	}
196	}
197
198	// TODO Provide this method in nanopub-java (GetNanopub)
199	private static Nanopub getNanopub(String uriOrArtifactCode) {
200	List<String> peerUrls = new ArrayList<>(Utils.getPeerUrls());	×
201	Collections.shuffle(peerUrls);	×
202	String ac = GetNanopub.getArtifactCode(uriOrArtifactCode);	×
203	if (!ac.startsWith(RdfModule.MODULE_ID)) {	×
204	throw new IllegalArgumentException("Not a trusty URI of type RA");	×
205	}
206	while (!peerUrls.isEmpty()) {	×
207	String peerUrl = peerUrls.removeFirst();	×
208	try {
209	Nanopub np = get(ac, peerUrl, NanopubUtils.getHttpClient());	×
210	if (np != null) {	×
211	return np;	×
212	}
213	} catch (IOException \| RDF4JException \| MalformedNanopubException ex) {	×
214	// ignore
215	}	×
216	}	×
217	return null;	×
218	}
219
220	// TODO Provide this method in nanopub-java (GetNanopub)
221	private static Nanopub get(String artifactCode, String registryUrl, HttpClient httpClient)
222	throws IOException, RDF4JException, MalformedNanopubException {
223	HttpGet get = null;	×
224	// TODO Get in Jelly format:
225	String getUrl = registryUrl + "np/" + artifactCode;	×
226	try {
227	get = new HttpGet(getUrl);	×
228	} catch (IllegalArgumentException ex) {	×
229	throw new IOException("invalid URL: " + getUrl);	×
230	}	×
231	get.setHeader("Accept", "application/trig");	×
232	InputStream in = null;	×
233	try {
234	HttpResponse resp = httpClient.execute(get);	×
235	if (!wasSuccessful(resp)) {	×
236	EntityUtils.consumeQuietly(resp.getEntity());	×
237	throw new IOException(resp.getStatusLine().toString());	×
238	}
239	in = resp.getEntity().getContent();	×
240	Nanopub nanopub = new NanopubImpl(in, RDFFormat.TRIG);	×
241	if (!TrustyNanopubUtils.isValidTrustyNanopub(nanopub)) {	×
242	throw new MalformedNanopubException("Nanopub is not trusty");	×
243	}
244	return nanopub;	×
245	} finally {
246	if (in != null) in.close();	×
247	}
248	}
249
250	private static boolean wasSuccessful(HttpResponse resp) {
251	int c = resp.getStatusLine().getStatusCode();	×
252	return c >= 200 && c < 300;	×
253	}
254
255	}

knowledgepixels / nanopub-registry / 23541488268

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