22870977169

Committed 09 Mar 2026 07:28PM UTC coverage: 27.117% (+1.6%) from 25.557%

Build # 22870977169

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push

github

Committed by

web-flow

Commit Message

Merge pull request #75 from knowledgepixels/74-peer-registry-sync

feat: add registry-to-registry peer sync for CHECK_NEW

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3.21

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;
        }
        String pubkeyHash = Utils.getHash(pubkey);
        // TODO Do we need to load anything else here, into the other DB collections?
        if (has(mongoSession, "lists", new Document("pubkey", pubkeyHash).append("type", "$").append("status", "loaded"))) {
            RegistryDB.loadNanopub(mongoSession, np, pubkeyHash, "$");
        } else if (has(mongoSession, "lists", new Document("pubkey", pubkeyHash).append("type", INTRO_TYPE_HASH).append("status", "loaded"))) {
            RegistryDB.loadNanopub(mongoSession, np, 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) {
        // 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";
            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();
            } 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	String pubkeyHash = Utils.getHash(pubkey);	×
69	// TODO Do we need to load anything else here, into the other DB collections?
70	if (has(mongoSession, "lists", new Document("pubkey", pubkeyHash).append("type", "$").append("status", "loaded"))) {	×
71	RegistryDB.loadNanopub(mongoSession, np, pubkeyHash, "$");	×
72	} else if (has(mongoSession, "lists", new Document("pubkey", pubkeyHash).append("type", INTRO_TYPE_HASH).append("status", "loaded"))) {	×
73	RegistryDB.loadNanopub(mongoSession, np, pubkeyHash, INTRO_TYPE, ENDORSE_TYPE);	×
74	} else if (!has(mongoSession, "lists", new Document("pubkey", pubkeyHash).append("type", INTRO_TYPE_HASH))) {	×
75	// Unknown pubkey: create encountered intro list so RUN_OPTIONAL_LOAD picks it up
76	try {
77	insert(mongoSession, "lists", new Document("pubkey", pubkeyHash)	×
78	.append("type", INTRO_TYPE_HASH)	×
79	.append("status", EntryStatus.encountered.getValue()));	×
80	} catch (MongoWriteException e) {	×
81	if (e.getError().getCategory() != ErrorCategory.DUPLICATE_KEY) throw e;	×
82	}	×
83	}
84	}	×
85
86	/**
87	* Retrieve Nanopubs from the peers of this Nanopub Registry.
88	*
89	* @param typeHash The hash of the type of the Nanopub to retrieve.
90	* @param pubkeyHash The hash of the pubkey of the Nanopub to retrieve.
91	* @return A stream of MaybeNanopub objects, or an empty stream if no peer is available.
92	*/
93	public static Stream<MaybeNanopub> retrieveNanopubsFromPeers(String typeHash, String pubkeyHash) {
94	// TODO Move the code of this method to nanopub-java library.
95
96	List<String> peerUrlsToTry = new ArrayList<>(Utils.getPeerUrls());	×
97	Collections.shuffle(peerUrlsToTry);	×
98	while (!peerUrlsToTry.isEmpty()) {	×
99	String peerUrl = peerUrlsToTry.removeFirst();	×
100
101	String requestUrl = peerUrl + "list/" + pubkeyHash + "/" + typeHash + ".jelly";	×
102	log.info("Request: {}", requestUrl);	×
103	try {
104	CloseableHttpResponse resp = NanopubUtils.getHttpClient().execute(new HttpGet(requestUrl));	×
105	int httpStatus = resp.getStatusLine().getStatusCode();	×
106	if (httpStatus < 200 \|\| httpStatus >= 300) {	×
107	log.info("Request failed: {} {}", peerUrl, httpStatus);	×
108	EntityUtils.consumeQuietly(resp.getEntity());	×
109	continue;	×
110	}
111	Header nrStatus = resp.getFirstHeader("Nanopub-Registry-Status");	×
112	if (nrStatus == null) {	×
113	log.info("Nanopub-Registry-Status header not found at: {}", peerUrl);	×
114	EntityUtils.consumeQuietly(resp.getEntity());	×
115	continue;	×
116	} else if (!nrStatus.getValue().equals("ready") && !nrStatus.getValue().equals("updating")) {	×
117	log.info("Peer in non-ready state: {} {}", peerUrl, nrStatus.getValue());	×
118	EntityUtils.consumeQuietly(resp.getEntity());	×
119	continue;	×
120	}
121	InputStream is = resp.getEntity().getContent();	×
122	return NanopubStream.fromByteStream(is).getAsNanopubs();	×
123	} catch (UnsupportedOperationException \| IOException ex) {	×
124	log.info("Request failed: ", ex);	×
125	}
126	}	×
127	return Stream.empty();	×
128	}
129
130	public static Nanopub retrieveNanopub(ClientSession mongoSession, String nanopubId) {
131	Nanopub np = retrieveLocalNanopub(mongoSession, nanopubId);	×
132	int tryCount = 0;	×
133	while (np == null) {	×
134	if (tryCount > 10) {	×
135	throw new RuntimeException("Could not load nanopub: " + nanopubId);	×
136	} else if (tryCount > 0) {	×
137	try {
138	Thread.sleep(100);	×
139	} catch (InterruptedException ex) {	×
140	log.info("Thread was interrupted", ex);	×
141	}	×
142	}
143	log.info("Loading {}", nanopubId);	×
144
145	// TODO Reach out to other Nanopub Registries here:
146	np = getNanopub(nanopubId);	×
147	if (np != null) {	×
148	RegistryDB.loadNanopub(mongoSession, np);	×
149	} else {
150	tryCount = tryCount + 1;	×
151	}
152	}
153	return np;	×
154	}
155
156	public static Nanopub retrieveLocalNanopub(ClientSession mongoSession, String nanopubId) {
157	String ac = TrustyUriUtils.getArtifactCode(nanopubId);	×
158	MongoCursor<Document> cursor = RegistryDB.get(mongoSession, Collection.NANOPUBS.toString(), new Document("_id", ac));	×
159	if (!cursor.hasNext()) return null;	×
160	try {
161	// Parse from Jelly, not TriG (it's faster)
162	return JellyUtils.readFromDB(((Binary) cursor.next().get("jelly")).getData());	×
163	} catch (RDF4JException \| MalformedNanopubException ex) {	×
164	log.info("Exception reading Jelly", ex);	×
165	return null;	×
166	}
167	}
168
169	// TODO Provide this method in nanopub-java (GetNanopub)
170	private static Nanopub getNanopub(String uriOrArtifactCode) {
171	List<String> peerUrls = new ArrayList<>(Utils.getPeerUrls());	×
172	Collections.shuffle(peerUrls);	×
173	String ac = GetNanopub.getArtifactCode(uriOrArtifactCode);	×
174	if (!ac.startsWith(RdfModule.MODULE_ID)) {	×
175	throw new IllegalArgumentException("Not a trusty URI of type RA");	×
176	}
177	while (!peerUrls.isEmpty()) {	×
178	String peerUrl = peerUrls.removeFirst();	×
179	try {
180	Nanopub np = get(ac, peerUrl, NanopubUtils.getHttpClient());	×
181	if (np != null) {	×
182	return np;	×
183	}
184	} catch (IOException \| RDF4JException \| MalformedNanopubException ex) {	×
185	// ignore
186	}	×
187	}	×
188	return null;	×
189	}
190
191	// TODO Provide this method in nanopub-java (GetNanopub)
192	private static Nanopub get(String artifactCode, String registryUrl, HttpClient httpClient)
193	throws IOException, RDF4JException, MalformedNanopubException {
194	HttpGet get = null;	×
195	// TODO Get in Jelly format:
196	String getUrl = registryUrl + "np/" + artifactCode;	×
197	try {
198	get = new HttpGet(getUrl);	×
199	} catch (IllegalArgumentException ex) {	×
200	throw new IOException("invalid URL: " + getUrl);	×
201	}	×
202	get.setHeader("Accept", "application/trig");	×
203	InputStream in = null;	×
204	try {
205	HttpResponse resp = httpClient.execute(get);	×
206	if (!wasSuccessful(resp)) {	×
207	EntityUtils.consumeQuietly(resp.getEntity());	×
208	throw new IOException(resp.getStatusLine().toString());	×
209	}
210	in = resp.getEntity().getContent();	×
211	Nanopub nanopub = new NanopubImpl(in, RDFFormat.TRIG);	×
212	if (!TrustyNanopubUtils.isValidTrustyNanopub(nanopub)) {	×
213	throw new MalformedNanopubException("Nanopub is not trusty");	×
214	}
215	return nanopub;	×
216	} finally {
217	if (in != null) in.close();	×
218	}
219	}
220
221	private static boolean wasSuccessful(HttpResponse resp) {
222	int c = resp.getStatusLine().getStatusCode();	×
223	return c >= 200 && c < 300;	×
224	}
225
226	}

knowledgepixels / nanopub-registry / 22870977169

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